Autism-Related Gene Spotlight: CNTNAP2

EXECUTIVE SUMMARY: CNTNAP2 is a large gene near the end of chromosome 7 that encodes a cell-adhesion protein involved in distributing ion channels along axons (the long tails of nerve cells) and in attaching the fatty cells making up the myelin sheath to the surface of the axon. DIsruptions in this gene have been associated with autism, epilepsy, Tourette syndrome and other neurodevelopmental disorders. Variations at certain points within the gene that don't alter or disrupt its expression have also been associated with an increased likelihood of autism.

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Where is it?
Chromosome 7, in the 7q35 region (i.e., near the end of the long, lower arm of chromosome 7).

CNTNAP2 is, according to Entrez Gene, one of the largest single genes in the human genome; it's about 2.3 million base pairs long, taking up 1.5% of the total space on chromosome 7.

What does it do?
CNTNAP2 encodes a cell-adhesion protein called contactin-associated protein-like 2 (Caspr2), which is part of a superfamily of adhesion proteins specific to nerve cells called neurexins.

During development, Caspr2 plays an important role in organizing the long tail of the neuron, called the axon. Caspr2 directs certain types of voltage-gated potassium ion channels (i.e., channels that open or close in reponse to changes in membrane potential) to insert themselves into the axon's membrane at specific intervals; it also forms part of the junction between the axon and the fatty glial cells that form the myelin sheath around the axon, which both insulates the axon (like the rubber tubing around a wire insulates the wire) and allows the electrical current to travel faster, in a discontinuous, hopping ("saltatory") manner from node to node along the myelinated axon.

(Image adapted from

Wikipedia)
To allow the current to travel discontinuously, the fatty cells making up the myelin sheath leave small stretches of axon uncovered at regular intervals. These unmyelinated points are called the nodes of Ranvier, and it is at these nodes that Caspr2 plays its traffic-directing role.

(Node of Ranvier and surrounding regions; taken from Figure 4 in Poliak and Peles, 2003)

Caspr2 sits in the membrane of the axon in its juxtaparanodal region (which means, "the region right next to the region next to the node" in ScienceSpeak), where its cytoplasmic domain (the part of a membrane-spanning protein that's inside the cell) links up with potassium ion channels prior to their insertion in the membrane, and directs them to insert adjacent to the complex of adhesion proteins including Caspr2. This ensures that the potassium channels all cluster together in the juxtaparanodal region, rather than distribute themselves more or less evenly along the axon, as they would do without guidance from the adhesion proteins.
This superabundance of potassium ion channels near the nodes of Ranvier makes the nodes hypersensitive to membrane depolarization (which is mediated by traffic of ions, including potassium, into and out of the cell), which allows an action potential (the "firing" of a neuron that happens once it reaches a certain threshold level of membrane depolarization) to be transmitted from node to node more easily.

This gene may also play a role in organizing the layers of cortical tissue during development.

What mutant versions of this gene have been discovered?

Lots of different ones! Here are (some of) the mutations that have been described so far:

An exchange of genetic material between two chromosomes: 7q35 and 15q26.2, with the breakpoint on chromosome 7 occurring inside CNTNAP2 (in the 11th intron, or noncoding region), and the breakpoint on chromosome 15 occurring in a relatively ill-understood region that's hypothesized to be a gene. This translocation was found in three generations of Old Order Amish, and described in this article in the European Journal of Human Genetics. Depending on whether the translocation was balanced or not (i.e., whether there was any net gain or loss of genetic material), the people having this mutation might be completely healthy and neurotypical, or they might have severe problems and die young.

An autistic woman in Italy was found to be missing a large (12 million base pairs!) chunk of chromosome 7q33-q36; CNTNAP2 is contained within the deleted region.

An autistic boy in the Netherlands was found to have an inversion --- a break in the q arm of one of his copies of chromosome 7 that reversed the sequence of genes on the broken part when it repaired itself --- between regions 7q32.1 and 7q35. Parts of CNTNAP2 --- the promoter region, which is where the enzymes involved in DNA transcription (the first stage of gene expression) attach to the genome and begin transcription, and parts of intron 1 and exon 2, which also contain important regulatory sites --- have been moved to another chromosome entirely: chromosome 1q31.2.

A preschool-aged boy with seizures and autistic traits (but not enough to be diagnosed with an ASD) was found to have an inversion between regions 7q11.22 and 7q35. The break in 7q35 occurs within CNTNAP2, somewhere between exons 10 and 13.

Nine of eighteen Old Order Amish people with developmental disabilities and a childhood-onset form of epilepsy were found to have a deletion of a single nucleotide (#3709) in coding region 22 of CNTNAP2. The deletion was present in both copies of the gene.

A family in which several members (the father and both children) have Tourette syndrome, obsessive-compulsive disorder, or both, were found to have a complex rearrangement of genes on chromosomes 2 and 7, including some swapping of parts of genes between those two chromosomes. Among other things, part of a gene on chromosome 2 is inserted into CNTNAP2, in a noncoding region. The inserted part is very large (12 million bases, six times the size of CNTNAP2 itself).

In a fairly large sample of families including more than one autistic member, a single-nucleotide change --- a substitution of thymine for adenine --- at a position approximately one-quarter of the way between coding regions 2 and 3 of CNTNAP2 (in other words, in an intron, or noncoding region) was found to occur at somewhat higher rates in autistic children than in their nonautistic siblings. This was especially true if the mutation was inherited from the mother.

A study of 185 Han Chinese families found another single-nucleotide variation in a noncoding region of CNTNAP2 that's associated with an increased likelihood of having autism.

A study of families participating in the Autism Genetic Resource Exchange found several single-nucleotide changes near the end of the intron between exons (coding regions) 13 and 14 in CNTNAP2, where the presence of a variant nucleotide at one of four different positions (with variation at one site in particular, designated rs2710102, seeming to drive variation at the other three) was associated with delays in development of speech.

Three people (two of them siblings) who had undergone genetic testing for a separate mutation (in a gene called TCF4, the underexpression of which causes Pitt-Hopkins syndrome) were found to have deletions in CNTNAP2; the two siblings were missing exons 2-9, and the other person was missing exons 5-8, and had another mutation rendering a splice site (a place where various enzymes cut out those parts of a transcribed gene that are not needed in protein synthesis, and then join the remaining fragments back together) potentially invisible to splicing enzymes, which could mean that exon 10, also, has been functionally deleted.

How do these mutations affect protein function?

(Drawing of CNTNAP2 exons and the protein domains they encode taken from Zweier et al., 2009)

A mutation's effect on protein function depends on where it is in the gene. The color-coded map I posted at the top of this section shows what kind of protein domain each coding region of CNTNAP2 encodes, and what role each domain plays in the protein's overall function (to the extent that either of those things is known, which can vary a lot from gene to gene).

For instance, the deletions mentioned in this article --- exons 5-8 in one person, and exons 2-9 in the others --- include a large block of laminin G domains (exons 5-10) and all three of the discoidin-like (DISC) domains near the end of the (exons 2-4). Both of these groups are on the part of Caspr2 that reaches outside the cell, and are involved in binding to other proteins on other cells to join the two cells together. In the nervous system, the two types of cells likeliest to be joined together are neurons and glial cells, during myelination.

Another domain that's important to Caspr2 function is the PDZ-binding domain at the end of the cytoplasmic half of the protein. That domain binds to PDZ domains on potassium channels while they're free in the cytoplasm and guide them to embed in the cell membrane near Caspr2. 

The point mutation described in this article would lead to garbled (or non-)expression of exons 23 and 24, which encode the transmembrane domain (i.e., the part of the protein that is embedded in the cell membrane) and the PDZ-binding domain; absence of those domains from Caspr2 might prevent that protein from clustering the potassium channels near the node of Ranvier.


How common are they?
Most of the mutations described above --- the deletions and translocations --- are very rare, possibly even unique to the individuals or families in whom they were discovered.

However, some of the single-nucleotide polymorphisms (SNPs) --- the alteration of a single nucleotide base --- are fairly common. The polymorphism described in this article, the presence of thymine at a point in a noncoding region of CNTNAP2 where most people have adenine, is thought to occur in 36% of people.

So, while those variant alleles might be somewhat more common in people with autism than in people without it, there will still be lots of people without autism who also have those genotypes. The prevalence of autism being what it is, there are probably a lot more neurotypical people with a given polymorphism than there are autistic (or otherwise non-neurotypical) people.


Database entries for this gene: AutDB, Ensembl, Entrez Gene, GeneCards, Labome.org, Leiden Open Variation Database

Sources:
Arking, D., Cutler, D., Brune, C., Teslovich, T., West, K., Ikeda, M., Rea, A., Guy, M., Lin, S., & Cook Jr., E. (2008). A Common Genetic Variant in the Neurexin Superfamily Member CNTNAP2 Increases Familial Risk of Autism The American Journal of Human Genetics, 82 (1), 160-164 DOI: 10.1016/j.ajhg.2007.09.015

Bakkaloglu, B., O'Roak, B., Louvi, A., Gupta, A., Abelson, J., Morgan, T., Chawarska, K., Klin, A., Ercan-Sencicek, A., & Stillman, A. (2008). Molecular Cytogenetic Analysis and Resequencing of Contactin Associated Protein-Like 2 in Autism Spectrum Disorders The American Journal of Human Genetics, 82 (1), 165-173 DOI: 10.1016/j.ajhg.2007.09.017

Belloso, J., Bache, I., Guitart, M., Caballin, M., Halgren, C., Kirchhoff, M., Ropers, H., Tommerup, N., & Tümer, Z. (2007). Disruption of the CNTNAP2 gene in a t(7;15) translocation family without symptoms of Gilles de la Tourette syndrome European Journal of Human Genetics, 15 (6), 711-713 DOI: 10.1038/sj.ejhg.5201824

Poliak S, Gollan L, Martinez R, Custer A, Einheber S, Salzer JL, Trimmer JS, Shrager P, & Peles E (1999). Caspr2, a new member of the neurexin superfamily, is localized at the juxtaparanodes of myelinated axons and associates with K+ channels. Neuron, 24 (4), 1037-47 PMID: 10624965

Poliak, S., & Peles, E. (2003). The local differentiation of myelinated axons at nodes of Ranvier Nature Reviews Neuroscience, 4 (12), 968-980 DOI: 10.1038/nrn1253

Poot, M., Beyer, V., Schwaab, I., Damatova, N., Slot, R., Prothero, J., Holder, S., & Haaf, T. (2009). Disruption of CNTNAP2 and additional structural genome changes in a boy with speech delay and autism spectrum disorder neurogenetics, 11 (1), 81-89 DOI: 10.1007/s10048-009-0205-1

ROSSI, E., VERRI, A., PATRICELLI, M., DESTEFANI, V., RICCA, I., VETRO, A., CICCONE, R., GIORDA, R., TONIOLO, D., & MARASCHIO, P. (2008). A 12Mb deletion at 7q33–q35 associated with autism spectrum disorders and primary amenorrhea European Journal of Medical Genetics, 51 (6), 631-638 DOI: 10.1016/j.ejmg.2008.06.010

Strauss KA, Puffenberger EG, Huentelman MJ, Gottlieb S, Dobrin SE, Parod JM, Stephan DA, & Morton DH (2006). Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. The New England journal of medicine, 354 (13), 1370-7 PMID: 16571880

Verkerk AJ, Mathews CA, Joosse M, Eussen BH, Heutink P, Oostra BA, & Tourette Syndrome Association International Consortium for Genetics (2003). CNTNAP2 is disrupted in a family with Gilles de la Tourette syndrome and obsessive compulsive disorder. Genomics, 82 (1), 1-9 PMID: 12809671

Zweier, C., de Jong, E., Zweier, M., Orrico, A., Ousager, L., Collins, A., Bijlsma, E., Oortveld, M., Ekici, A., & Reis, A. (2009). CNTNAP2 and NRXN1 Are Mutated in Autosomal-Recessive Pitt-Hopkins-like Mental Retardation and Determine the Level of a Common Synaptic Protein in Drosophila The American Journal of Human Genetics, 85 (5), 655-666 DOI: 10.1016/j.ajhg.2009.10.004

"What Is High Functioning?" Tumblr

Someone (I think it was Amanda Forest Vivian, but I'm not sure) started a Tumblr for the purpose of providing highly specific answers to that question --- what is "high functioning"?

People are encouraged to submit anecdotes about people with developmental disabilities being labeled "high functioning," and what specific thing they think led the person to label them that way.

Some specific examples of things that get people sorted into the "high-functioning" category:

• Asking what it means to "exchange a look"
• Initiating a conversation with another student in a college dining hall
• Requesting a peanut-butter-and-banana sandwich in lieu of whatever food they've just been given

(There are also some less-concrete examples of "high-functioning" stuff like being able to speak fluently, carry on a conversation, not having a "routine" and being "independent.")

Anyone can submit a post; they just have to click the "Submit" link in the sidebar and type in the text of their post, a title, and their name and email address.

I love the idea around this Tumblr blog --- to have one place where people can share all the different things "high-functioning" has been used to mean --- and would submit an anecdote or two of my own if my autobiographical memory weren't only slightly better than Wolverine's. (I know that I've been called "high-functioning" fairly often --- at least once in the context of, "isn't she too high-functioning to be here (at a camp for autistic children)?" --- but cannot remember the details of any of these instances. So I don't think there's anything I could contribute that would be of value to this project, which is too bad).

Doubly Deviant: On Being Queer and Autistic

EXECUTIVE SUMMARY: This is a very long, rambly autobiographical post about being bisexual and being autistic: it compares my experiences coming to terms with both of these facts (always knowing about the autism, vs. having to figure out the sexual orientation; and also, doubting the possibility that I could *have* a sexual orientation because I thought autistic people didn't date or have sex, or even want to do either of those things) with those of Amanda Forest Vivian, who is a lesbian, and autistic, and has written about those things at some length at her own blog. I also discuss the ways being autistic has complicated being gay for me --- besides my initial difficulty realizing that what I felt about girls was, in fact, sexual desire, there was also a profound isolation from the larger Gay Community, which I never felt like I could (or would want to) join.
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Amanda Forest Vivian has a post from a while ago about this --- being gay (Amanda uses "same-sex attracted", to encompass lesbian, gay, bi-*, poly- and pansexual folk, and also people who don't really fit into any category but "queer"), but also being different in another way (like having a developmental disability) that might make it harder to navigate an LGBTQ** an LGB social scene.

Here's her description of coming out in high school ---

When I was in high school, someone who wasn't my friend said this to my (secret, closeted) friend, who then told me: "Everyone could see that something was different about Amanda, and then when they found out she was gay, they had an answer."

When I was in high school, the word dyke or lesbian was a way to easily quantify all the things about me that didn't seem right. When I was in high school I felt very alone.

When I was in ninth and tenth grade, I actually brought all this on myself by not denying that I was gay or bisexual, and presenting in a masculine way. I felt this was an important thing to do because other kids needed to see that queer people were just regular people. The problem with this idea is, in hindsight, obvious: I am not a regular person. Being openly queer in a heteronormative environment is a noble thing to do, but maybe not if you have anxiety about pretty much everything and have trouble talking to people.

A lot of my coming-out process happened when I was on a lot of medication and overwhelmed by the relationships I was in. By the time I was in eleventh grade, I was more able to clearly see what was going on, and I knew that I'd made a mistake by not being closeted. My school was very small, and some people were genuinely afraid to be friends with me in case someone said they were having sex with me, and I wasn't a person who could charm my way out of this stigma. But my school wasn't violently homophobic and I feel like a more normal person could have made a difference. It would have to be a person who fit in every way, except one.

--- which reminded me a lot of these much older posts by elmindreda and one of the other Amandas whose writing I love, Amanda Baggs, which postulate something called the "difference slot."

elmindreda:

[M]any of [the people I spend my time with nowadays], even though they seem superficially informed about basic disability issues, seem to believe in the difference slot.

The basic idea is that each and every person has their difference, and it should be respected. Note the singular form, however. When they learn of my autism, which is usually the first major difference to come up in conversation, they seem to think "oh, so that's her difference". They then proceed to fill in my difference slot in their mental table, and everything is as it should be.

Or so they think.

Then, a little while later, I happen to mention some other thing that makes me different from most other people, and their belief system collides head-on with reality. Usually, it's another one of my disabilities that triggers it. This is when they almost invariably go "..." for a while, only to finish with "you have that too?" In other words, "your difference slot is already filled, and you can't have another one."

Amanda (Baggs):

What I'm writing about is similar [to elmindreda's idea of the "difference slot"], but perhaps from a different angle. A phenomenon I've seen over and over again runs something more like, "Please violate only one stereotype at a time."

This can apply even if you have only one "difference" (be that autism, physical disability, whatever).

If you have several differences, of course, the problem becomes exponentially harder to deal with.

What Amanda Forest Vivian is describing --- being in a very normative environment (hetero- and otherwise) and trying to figure out, and come to terms with, how you deviate from those deeply-entrenched norms (which you do in multiple ways that you either cannot yet identify or are struggling to identify) --- sounds a lot like what elmindreda describes: the first difference you name to other people defines you, and explains Everything That's Weird About You, and people resist learning that there's more to the story than that One Thing That Explains Everything.

When you're very young, that first difference you name might not actually be the difference that's most relevant to your day-to-day life, either, but may simply be the first difference you know how to name. This is especially relevant to people whose differences are either a) internal or invisible, something you have to find out about yourself rather than something that's always been generally known about you or b) disabilities that affect your ability to put things into words, or even recognize all the ways in which you differ from most people. (Cultural differences might also factor into (b) --- if you come from a culture that does not discriminate between X sorts of people and Y sorts of people, and you immigrate into a culture that does, you may find that you don't even know whether you're X or Y, and that makes it difficult for you to navigate a social setting in which lots of important stuff hinges on whether you're X or Y.)

I had almost the opposite experience from Amanda's --- my first difference was my autism, which has been generally known about, and accommodated, and I've been able, to varying degrees, to talk about, for as far back as I can remember. As long as I remember being able to think in terms of "me" and "you" and "them" (which for me happened rather later than for most people, I suspect), I knew that I had a thing called autism which meant I was different from most people. As I grew older, I came to understand how I was different, and to be able to tell other people about it, but I always knew that I was different.

I had a very elastic understanding of this difference of mine, probably because I learned I was autistic before I could have any real idea what "autistic" meant, so I pretty much equated it with "whatever I am," adding on "whatever [other autistic person I meet] is, too".

(I had always had plenty of contact with other autistic children, both older and younger, and I also always had books written by autistic people about their lives on hand, so I never really fell into the "autism is *ONLY* what I experience" trap that some autistic people fall into --- it seems to be the flip side of the "impostor syndrome" that many later-diagnosed autistics have).

So, for me, being queer was the late-manifesting difference that made it harder to quickly and easily account for everything odd about me, and accordingly I had tons of self-doubt when I first started wondering if maybe I was gay.

My relative lack of interest in boys (had one crush in middle school, on a long-haired androgynous-looking boy) as I was going through puberty didn't tell me anything --- after all, I was autistic! By this time, I had come to understand a bit of what "autistic" meant, and one of those things --- communicated mostly by my mom's not thinking it a priority to educate me about sex and relationships --- was that I might never have sexual feelings, or act on them if I did. This was a boon in some ways: I was never assumed to be straight, exactly, and it was never taken for granted that I would marry by age twenty- or thirty-whatever and have x number of children. I was allowed to develop sexually at my own pace, and in my own direction, rather than feeling like I had to fit a mold. But, at the same time, since I wasn't assumed to be a sexual being, I felt like I couldn't really be sure that the things I was feeling were sexual feelings. So maybe I *did* expect to fit a mold, but that mold was asexuality rather than monogamous, married heterosexuality.

Accordingly, I waited to come out until I had clear, unmistakable evidence that I was gay: a really intense, serious crush on a female friend of mine who was bisexual and "out" about it.

Once I was absolutely certain I felt "that way," however, I thought nothing of telling people so if it came up in conversation. (I never lied, or tried to hide it from anybody, but then neither did I feel like I had to go around telling everyone I knew that I was now a lesbian. Either they'd find out sooner or later, or they didn't need to know).

It did surprise me, though, when in my last year of college I ran into a girl who'd been in my high-school graduating class --- whom I hadn't really known all that well; we went to a huge high school and knew each other by sight and by name, but never talked much and weren't friends --- and she told me that she, and a whole group of other people I didn't know or didn't know very well, apparently thought I was probably a lesbian. This surprised me because, as I mentioned, I was only really "out" to my friends --- the people I talked to enough that it eventually came up --- and I had figured I was more or less invisible to the rest of the school. So apparently I differed from whatever my high-school culture considered a "normal girl" enough, and in enough of the right ways, that people would think I must be a lesbian without ever having heard me say it. Either that, or they noticed me sticking around the girl I loved like I was actually glued to her side, and figured I must be on rather more than just "friendly" terms with her*** ...

I was also not the only lesbian, gay or bisexual person at my high school, either, so I had none of the anxiety that Amanda describes about being the Queer Model Citizen who shows everybody that queer people are people just like everybody else. If people needed that lesson, there were lots of people at my school who were better qualified (i.e., more charismatic, more involved, more flamboyantly out) than I was and more eager to do it besides.

Here, from later in the post, is the part of Amanda's story that most closely matched my own:

Even though my school is ssa-positive, most of the people at my school are straight just like most of the people in the world. I have enough friends that I never feel lonely, but I don't belong to a group of friends (partly because I don't like groups), and I know very few ssa people because I don't have stereotypical queer interests.

A few years ago I posted on a lesbian advice forum saying I was depressed and stressed because I wanted to believe I would someday get married and have kids, but that I had never been in a relationship and didn't think I ever would be. People responded telling me that if I was on a date with a girl, I shouldn't tell her I wanted to have kids, because she would think I was creepy. One person went to my livejournal, saw where I went to school, and told me that my school wasn't anyplace to complain about and that I should "stop whining." She provided a list of various social groups and activities that would help me to meet "dykes," including eating in a co-op (which would mean being organized enough to eat at the same time every day, taking up a lot of executive function cooking and cleaning, and constantly interacting with a large group of people I didn't know).

While there are a few differences --- I don't want kids, and I never got depressingly counterproductive advice because I never thought to ask for advice in the first place --- this sort of inability to find other queer women even on a campus with a burgeoning, vibrant queer culture (well, for Kansas anyway --- I went to KU, which, while it might look straitlaced and boring to someone from California, does have a fair amount of gay-themed student activities) is exactly what I experienced at college, too.

I wasn't closeted, and I wasn't isolated in general --- I just needed to socialize on my own terms, one on one with people I met in classes or in the dorms (or, sometimes, at the gym, which was my other main on-campus haunt), which might eventually lead to me joining a group of friends, rather than trying to meet people at huge gatherings of strangers (like a party or student club; I've never been much of a "joiner" because of my tendency to fade into the background and not enjoy myself at group events), so this ruled out my meeting other lesbian and bisexual women through formal channels, like the campus Queers & Allies club or gay-oriented parties and bars. Unfortunately, the informal, one-on-one processes I used to make friends --- and which worked really well in that regard --- never linked me up with any queer women. So I went through college knowing that lesbian and bisexual women were around, but I just wasn't meeting them.

Rather than belong to a lesbian or queer community, I just existed as a lesbian. (I didn't know I was bisexual until later in college). What I had growing up as an autistic person --- personal acquaintance with a number of other autistic children, access to autistic adults' life stories --- I did not have when I was coming out as a lesbian. I knew I liked women, but never met anyone who might reciprocate those feelings.

What compounded my isolation was my total lack of anything resembling gaydar. I really do have the inability to "read" faces, body language, tones of voice etc. that has become a stereotypical characteristic of autism, so I need to be literally told 1) that a given person is gay or bisexual or 2) that a person is attracted to me. I neither flirt nor perceive flirting in another person, which might well have told an unknown number of interested lesbians that I wouldn't welcome their attentions.

So when Amanda says this ---

I used to have a political problem with the way other ssa people behaved. Whenever I thought about it I got so upset I didn't know what to do. The way I saw it, there were two kinds of ssa people:

1. "gay" people (such as people involved in the HRC) who were very normal and wanted to have normal jobs and normal families. They didn't think much about trans people, non-homosexual sexual minorities, or anyone who wasn't normal.

2. "queer" people (such as a lot of people at my school) who were very into not being normal, playing rugby, performance art, co-ops, and so on. Many of them identified as trans but didn't seem to realize that some trans people actually take hormones and get surgery and are poor, and are not students at a liberal arts college who change their pronouns every week.
...
I felt weird because I wanted to get married but I wasn't normal and I felt like "gay" people wanted to help normal people get married and "queer" people were anti-marriage so neither one included me.

--- I nod because the feeling of not belonging, of not finding what one is looking for in a group, is familiar to me, even if the actual dynamics of gay-identified versus queer-identified groups fall far outside my own experience, which is of near-total**** isolation from other women attracted to women, whatever their chosen label or subculture*****.

*According to Genderbitch, it's actually possible to be bisexual (attracted to people belonging to either of two sexes) without one of the categories you're attracted to being the same as your own. When you consider a broader spectrum than just cis men and cis women --- one that includes trans men, trans women, non-binary trans people, intersex people and people in whatever other sex-and-gender categories there might be --- a bisexual person might be attracted to people in any two of these categories. So not every bisexual person necessarily fits under Amanda's "same-sex-attracted" umbrella, but I do (having so far only been attracted to cis women and cis men) and this post is about Amanda's (who is a cis lesbian) experience and mine.

**Edited to reflect a lesbian trans woman and an aspie's criticism in comments that, since I am talking about cis lesbian/bisexual stuff, I shouldn't use "LGBTQ" because it implies an inclusion of trans people that isn't in the post.

***I wasn't, as a matter of fact. I was in love with her, and told her so repeatedly, but she didn't love me. At least, not in a romantic way. We did come to be pretty good friends, though, even after high school!

****I did meet one other lesbian at college, whom I found nice, and attractive, and would certainly have befriended and quite likely have dated if we had ever met again. We just ran into each other one day, outside the dining hall, started talking, and kept talking for a long time eating lunch together. Then we went our separate ways and never bumped into each other again. She played rugby, and tried to interest me in joining, but I was unsure about how much extra time I could spare for practices --- I always took really heavy courseloads, tried to keep my GPA pretty high, and spent one to two hours in the gym every day. I figured if I did much more, I'd feel like I was stretched too thin. So, while I had good reasons for not wanting to add another commitment, I still feel sad about missing that particular opportunity. :(

*****Had I managed to fall in with the Queer Culture Amanda describes, I would probably have found it a more comfortable fit than she did, since the kind of alternative family structures she says they liked to try to create are just the sort of thing I'm looking for: I need kind of a lot of support, day to day, and don't think any one person could be everything I need and also have a life of hir own. So a poly family actually looks really good to me, and indeed my last relationship did somewhat resemble this.

New Series: Autism-Related Gene Spotlight

With this entry, I'm starting a new series of posts: the Autism-Related Gene Spotlight series.

Each post will talk about a different gene that's been identified as possibly having something to do with autism, and will follow more or less the same format.

I ask, and answer, five questions about the gene I'm spotlighting:
1) Where is it? - which chromosome, approximately where on the chromosome, how much space it takes up
2) What does it do? - which should probably read "What does the protein it encodes do," since genes typically don't do things themselves, but rather direct the synthesis of proteins which do things, but whatever.
3) What mutant versions of this gene have been discovered?
4) How do the mutations referred to in 3) affect the expression, structure and function of the gene's protein product?
and 5) How common are each of the mutations identified in 3)?

I will also link to whatever database entries I can find for the gene, so that readers with the training to decipher this stuff on their own can go have a look for themselves.

I'm excited about this series because this is the kind of stuff I studied in college, and I really love feeling like I understand things --- physical processes --- at the smallest level of detail. It's like when you're drawing a picture of something from life --- a tree or a flower, say --- and you've got the overall shape of it sketched out but you have to move in closer to see the details, to know what sort of texture to give the surfaces, and you see another layer of structure, something you couldn't see from farther away but which makes what you had perceived as texture make sense now that you see more of what it's doing.

I'll try to keep the jargon to a minimum, and provide explanations of whatever comes up that needs explaining (in the last post, I had to greatly expand my "What does [SLC4A10] do?" section to explain some things about acid-base chemistry, active transport and the special role ions play in "excitable" cells like neurons), but let me know if my attempts at making this stuff accessible don't go far enough.

Autism-Related Gene Spotlight: SLC4A10

EXECUTIVE SUMMARY: SLC4A10 is a member of a large family of genes that encode proteins for transporting ions (charged particles) across cell membranes. Within that (super)family, SLC4A10 belongs to a family of transporter proteins specializing in bicarbonate (HCO₃^-) ion transport, which is important for maintaining a constant pH within the cell --- i.e., preventing it from becoming too acidic or basic for the cell's biological machinery to function. SLC4A10 encodes a version of this transporter protein specific to certain cells of the central nervous system, and mutations disrupting this gene have been found in two instances: first, in a set of autistic twins who participated in a genomic study, and second, in a girl with epilepsy and intellectual disability. Disruption of this gene is thought to make brain cells more excitable, which can lead to seizures (which is probably why the girl in the second case study has them).
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Where is it?
Its "cytogenetic band" is given as 2q23-q24 (or, alternatively, 2q24.2), which means that it's on the long arm ("q" as opposed to "p") of chromosome 2, somewhere in the middle.

Here's a map of chromosome 2, with a red line marking where SLC4A10 is:
This gene spans 360,942 base pairs (which is fairly large, but not enormous; there's a lot of variability in gene size, with the smallest ones only a few hundred bases long and the largest spanning several million bases --- see this e-textbook chapter for details), covering the distance between bases 162,480,845 and 162,841,786 (measuring from the centromere to the end of the chromosome).


What does it do?
The name SLC4A10 refers to its membership in a family of genes encoding similar proteins: solute carrier family (SLC) 4, which is a group of ten genes whose protein products transport bicarbonate ions (HCO₃^-) across cell membranes.

Bicarbonate ion (and its protonated form, carbonic acid, which is readily synthesized from carbon dioxide and hydrogen ions) plays a central role in regulating pH, both within cells and outside of them, as in blood. pH is a measure of acidity, expressed as the (negative) logarithm of the concentration of hydrogen ions (H⁺) in the fluid being tested. Pure water has a "neutral" pH of 7 (meaning that, of the H₂O molecules making up liquid water, an approximately equal number exist in their dissociated forms of H⁺ and ^-OH at any given time --- if an acidic or basic compound is added, it will either add or remove H+ to the solution, and thus move the pH down or up); the water inside human bodies is slightly basic and has a pH of around 7.4 ("physiological pH"). Bicarbonate/carbon dioxide can act as a "buffer" between an acidic or basic substance and the physiological environment: depending on what form it's in, it can either donate (H₂CO₃ --> HCO₃^- --> CO₃^2-) or receive (CO₃^2- --> HCO₃^- --> H₂CO₃) hydrogen ions and keep the surrounding fluid from having to disrupt its acid-base equilibrium.

Because bicarbonate cannot diffuse across cell membranes by itself, it needs to be transported into cells by ion-exchanging membrane proteins whenever it is needed. The protein produced by SLC4A10 ferries bicarbonate ion and sodium ion into the cell while expelling a chloride ion from the cell. Two bicarbonate ions are imported for every sodium ion, which keeps the net gain/loss of electrical charge at zero.

This particular gene is primarily expressed in the central nervous system (i.e., the brain and spinal cord), though related genes encode similar bicarbonate-transporting proteins for other tissue types. In mice, SLC4A10 is expressed in some types of brain tissue but not in others: it was specific to gray matter (neurons, but not glial cells), and was not expressed in white matter; and it was also specific to certain regions of the brain: the olfactory bulb, cortex, hippocampus and cerebellum.

In neurons, ion concentrations inside and outside the cell play a role in whether a given neuron will "fire" --- undergo dramatic and rapid change in the electrical potential difference across its membrane, which triggers electrical and/or chemical signaling of adjacent neurons --- so ion transporters in neurons also help mediate neurotransmission.

What mutant versions of this gene have been discovered?
In the article I mentioned in my last post --- Sebat et al., 2007 (full text here) --- the authors report finding a spontaneous deletion of the first coding region of SLC4A10 in a pair of twin girls with autism.

There is also a recent report of a girl with epilepsy and intellectual disability having part of this gene --- a 48,000-base stretch of the 2q24 region falling between coding regions 2 and 3 of SLC4A10 --- moved to another chromosome: chromosome 13.


How do these mutations affect protein function?
Mice bred with the entire SLC4A10 gene missing were found to have much smaller brain ventricles than normal mice, and also had altered choroid plexus tissue. (The choroid plexus is where cerebrospinal fluid is made and waste is filtered out of it; active-transport proteins are especially dense there). Researchers found it harder to induce seizures in these mice as compared with normal mice using the proconvulsant (i.e., seizure-inducing) drugs pentylenetetrazole and pilocarpine.

Neither of the mutations observed in humans involves knocking out the entire gene; one involves deleting the first (of twenty-six) coding region, and the other involves switching a fairly long non-coding region with a sequence from another chromosome. Nothing is deleted in that case, but the insertion of something random into the middle of a gene might derail the process of assembling a working protein using that gene's (garbled) instructions. So both mutations impair the production of this protein to an unknown degree --- the protein probably isn't completely absent, but it might be present in reduced quantities or truncated, less-than-fully-functional form.
How common are they?
Very rare. Mutations in this gene are probably only a factor for a tiny, tiny minority of autistic people, whom I would suspect also have seizures.

Database entries for this gene: AutDB, Entrez Gene, Ensembl, Genatlas, GeneCards, SFARI Gene
Sources:
Damkier, H., Aalkjaer, C., & Praetorius, J. (2010). Na+-dependent HCOFormula Import by the slc4a10 Gene Product Involves Cl- Export Journal of Biological Chemistry, 285 (35), 26998-27007 DOI: 10.1074/jbc.M110.108712

Gurnett CA, Veile R, Zempel J, Blackburn L, Lovett M, & Bowcock A (2008). Disruption of sodium bicarbonate transporter SLC4A10 in a patient with complex partial epilepsy and mental retardation. Archives of neurology, 65 (4), 550-553 PMID: 18413482

Jacobs, S., Ruusuvuori, E., Sipila, S., Haapanen, A., Damkier, H., Kurth, I., Hentschke, M., Schweizer, M., Rudhard, Y., Laatikainen, L., Tyynela, J., Praetorius, J., Voipio, J., & Hubner, C. (2008). Mice with targeted Slc4a10 gene disruption have small brain ventricles and show reduced neuronal excitability Proceedings of the National Academy of Sciences, 105 (1), 311-316 DOI: 10.1073/pnas.0705487105

Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., Leotta, A., Pai, D., Zhang, R., Lee, Y., Hicks, J., Spence, S., Lee, A., Puura, K., Lehtimaki, T., Ledbetter, D., Gregersen, P., Bregman, J., Sutcliffe, J., Jobanputra, V., Chung, W., Warburton, D., King, M., Skuse, D., Geschwind, D., Gilliam, T., Ye, K., & Wigler, M. (2007). Strong Association of De Novo Copy Number Mutations with Autism Science, 316 (5823), 445-449 DOI: 10.1126/science.1138659

Autism and Genetics: It's Complicated

EXECUTIVE SUMMARY: Evidence from a 2007 genomic study of 264 families (118 with one autistic member, 47 with multiple autistic members, and 99 with no autistic members) suggests that all autistic people have a higher rate of spontaneous --- i.e., not inherited --- mutation in their genomes than non-autistic people, and autistic people without autistic relatives have the highest rate of such mutations.
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Though most autism researchers believe autism is at least partly determined by genetics --- it co-occurs most of the time in identical twins, and a higher-than-baseline proportion of the time in fraternal twins and non-twin siblings --- they haven't really been able to find genetic variations that account for more than a small minority of cases of autism.

Here's an illustration of that paucity of known genetic explanations for autism:

Graph from Arthur L. Beaudet's editorial in the May 2007 issue of Nature Medicine. The darkest-colored regions (both pink and blue) represent the proportion of instances of autism that are totally unexplained; the lightest-colored regions represent instances of autism known to be caused by a particular genetic mutation; regions between the lightest and darkest regions represent those instances of autism where there may not be any definitive genetic cause, but a genetic cause is considered likely

It's not that candidate genes aren't showing up; it's just that each mutation found that seems like it might underlie some aspect of autism is only present in a tiny, tiny fraction of all autistic people. Variations in a whole lot of different genes have been implicated in some cases of autism some of the time, but a genetic marker common to all (or even most) autistic people that's not also found in general population remains elusive.

This article in Science (full text here) from a few years ago adds more ambiguity to the whole mess: its authors (all thirty-two of them!) found a certain type of large-scale mutation called a copy-number variation (i.e., a given region of the genome is either missing, or repeated one or more times in a row) occurring about ten times as frequently in the autistic population whose DNA they sampled (n = 118) as in the non-autistic controls (n = 196), and a little more than three times as frequently as they occur in autistic people with another autistic person in their immediate family (n = 77).

They were able to see the copy-number variations using a type of comparative genomic hybridization called representational oligonucleotide microarray analysis (ROMA). (See this full-text article in Genome Research for a detailed description, and discussion, of this method of genomic hybridization).

Genomic hybridization, in general, is used to detect large-scale differences between a DNA sample of interest (usually, DNA taken from a tumor cell) and a reference sample. Both samples of DNA are tagged with small molecules that fluoresce in different colors, denatured (i.e., heated to a point where the strands untangle from one another), and added either to a sample of normal human chromosomes taken from cells that are just about to divide --- i.e., the paired chromosomes have split --- or to a slide covered in smaller DNA probes, or lengths of bases snipped from a reference sample of human genomic DNA at regular intervals. Given enough time, the denatured experimental and reference DNA samples will try to pair up ("hybridize") with the probe DNA that has been provided to them. When that happens, you can wash off all the single-stranded and unmoored double-stranded DNA (leaving only DNA that has hybridized to your probes, which are attached to a glass slide or microarray) and look at the radiation being emitted by the DNA left on the slide (using a fluorescence microscope or a spectrophotometer). Depending on what kind of copy-number variations (if any) are present in your sample, it will affect what color light you see more of. If you have a deletion of all or part of the genome regions represented by your probes*, the sample won't hybridize there, or it will hybridize very weakly, so you'll see a preponderance of whatever color you've chosen for your reference sample. Conversely, if a sequence of DNA is repeated in your sample, more of the experimental DNA than reference DNA will be able to hybridize to the (limited number of) probes, and the color you'll see will reflect that.

Now, ROMA differs from standard-issue microarray-based comparative genomic hybridization in one key way: instead of using a whole genome as a sample, it cuts up the genome with restriction endonucleases (enzymes for cutting up DNA that occur naturally in bacteria), amplifies the enzyme-digested sample (i.e., makes lots and lots of copies of it, with the help of a different bacteria-derived enzyme), and hybridizes these short fragments (called "representations") to a microarray probe equipped with short sequences designed to be complementary to the fragments. According to the researchers who created this method, using representative fragments instead of whole genomes allows for the detection of copy-number variations on a smaller scale than was previously possible.

Anyway, that's the method of genomic analysis these researchers used. (Several of them, including the lead researcher, Jonathan Sebat, were on the team that pioneered ROMA in that aforementioned article.) There's a lot more detail about their methods here, in the Supporting Online Material, if there's anything you're curious about that I didn't address.

The weird thing about this research, the thing I wanted to point out as complicating the notion of autism-as-inherited-genetic-variation, was the fact that all of the copy-number variations they found, the ones that were present so much more frequently in autistic people without a similarly-affected relative, were de novo --- not inherited, but spontaneously arising during embryonic development. (In fact, inherited copy-number variations --- those found in both parents and children --- were left out of the statistical analysis. The researchers wanted to highlight de novo mutations).

From the article:

Our findings have implications for an understanding of the genetic basis for ASDs. An important feature of the de novo CNVs we report is that each is individually rare in the population of patients. None of the genomic variants we detected were observed more than twice in our sample, and most were seen but once. Although our sample size is small, these results suggest that lesions at many different loci can contribute to autism, a result consistent with the findings from cytogenetics, as well as consistent with the failure to find common heritable variants with a major effect on disease risk. Lack of recurrence may in fact reflect an underlying reality that autistic behavior can result from many different genetic defects. This would be consistent with the hypothesis that the common features of autism such as failure to develop social skills and repetitive and obsessive behavior may in fact be the consequence of a reaction to many different cognitive impairments, drawing their "commonality" from a normal but maladaptive programmed response of humans early in development to those diverse impairments.
...
We can incorporate a high rate of spontaneous mutation in a genetic model that accounts for both sporadic and familial forms of the disease, based on new mutations that cause autism by haploinsufficiency [Wikipedia link] but have incomplete penetrance, especially in females. Such individuals who escape the phenotypic consequences can then pass on the mutation ... .

(Yes, there's an awful lot of pathologizing language in this excerpt. Sorry about that. The talk of "genetic defects" and such sets my Eugenics Radar a-pinging, and that's never a good sign.)

I also have no idea what is meant by that last sentence of the first paragraph, which attempts to explain the diverse genotypes all leading to one common phenotype, which we call autism. That's the biggest thing that confuses me about the size and heterogeneity of the pool of mutations that have been found in all the various genetic studies of autism --- how can all these different mutations lead to the same thing? This concern is somewhat mitigated by my knowledge of how imprecisely "autism" is defined, and the fact that it's defined behaviorally rather than physiologically.

While these findings of high rates of spontaneous mutation associated with autism do add another layer of complexity to the what-causes-autism debate ("It's genetic!" "It's acquired sometime during gestation!" "It's both!!"), they also make sense out of a lot of things. Foremost, it accounts for the lack of any one heritable mutation common to all (or most, or even a large minority of) autistic people, and the vast array of mutations occurring in individual autistic people.

It also makes the (what I assume to be**) relatively uniform proportion of autistic people in human populations across space and time make a bit more sense --- if it was mostly inherited, you would expect populations that are reproductively isolated from one another to diverge in their relative levels of this trait, as they do in other traits. But the rate of spontaneous mutation is more or less constant.

*or, if you're using chromosomal cGH, anywhere at all, so long as the deletion is big enough to matter at that level of analysis.

**Judging from the smattering of cross-cultural studies of autism prevalence I've read

Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., Leotta, A., Pai, D., Zhang, R., Lee, Y., Hicks, J., Spence, S., Lee, A., Puura, K., Lehtimaki, T., Ledbetter, D., Gregersen, P., Bregman, J., Sutcliffe, J., Jobanputra, V., Chung, W., Warburton, D., King, M., Skuse, D., Geschwind, D., Gilliam, T., Ye, K., & Wigler, M. (2007). Strong Association of De Novo Copy Number Mutations with Autism Science, 316 (5823), 445-449 DOI: 10.1126/science.1138659

Stop, Look and Listen --- It's Autistics Speaking Day

First, a little background information:

Today, there's something going on called Communication Shutdown, in which people are encouraged to abstain from Facebook and Twitter all day to 1) raise awareness of autism --- while users are offline today, their pages will display an icon that explains why they're offline; 2) simulate what it's like being autistic, i.e. being cut off from the wide world of social communication; and 3) raise money for various autism charities around the globe via participant donations.

(For a brief, but really enlightening, discussion of why autism charities are problematic, see this post on Cripchick's blog).

Lots of autistic bloggers, Facebook and/or Twitter users are annoyed with this autism-awareness campaign, partly because abstaining from social media isn't very enlightening as far as what it's like to be autistic.

Social media and the Internet actually represent ways autistic people connect with others, to a greater extent than we can in our non-digital lives. The Internet has allowed us to meet other autistic people around the world, talk about issues that are important to us, commiserate and empathize with each other over things that non-autistic people --- however kind or well-intentioned --- just don't understand. Social media can enable us to maintain friendships across distances that we might not be able to cross in the physical world, since autistic people are often unable to travel as freely as non-autistic people to whom driving a car, riding a bus cross-country or flying on an airplane and navigating a busy airport do not constitute serious challenges.

So, for some autistic people, a better awareness campaign would be something like Corina Becker's idea: Autistics Speaking Day, in which autistic people take to their blogs, Facebook pages and Twitter accounts to write about what it's like to be autistic.

Let us use this day to flood every social networking site we know with our accounts, our experiences, what it feels like to be Autistic.

Every sensory pain, every communication frustration, every account of being bullied, every wondrous moment, every peaceful calm, every instant of understanding and joy.

Let them hear our voices and take back the Autism community.

Let us speak.

Let us tell you what it's like to be us.

And that, would be true Autism Awareness.

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For Me to Speak, You Have to Listen.

Sometimes, people with disabilities need more space than people without disabilities do. This applies not just to physical spaces --- aisles, car and bus interiors, seating, sidewalks, doorways, hallways, etc. --- that need to be broad enough to accommodate wheelchairs, walkers, scooters, service animals, or other mobility and assistive devices, but also to interpersonal spaces.

A conversation can be accessible or inaccessible, just like a building can be. Just like there are places where only people who can do certain (physical) things --- climb stairs, squeeze through narrow openings, open heavy doors, etc. --- can go, so are there social and political environments where only people who can do certain (verbal, mental, emotional) things can participate.

You have to be able to speak, loudly and rapidly. Most of the time, you'll need to be able to control your need for pauses, for breathing or thinking space, so that you can get a complete thought out in one piece. You have to be able to intellectualize --- not to get so upset that you become incoherent, which can be hard if the issues being discussed have a direct bearing on your life. You also can't be too intellectual, or you'll lose your audience. You can't talk for too long. You can't be too abrupt. You have to be able to see where the conversation is going, as if it were a living thing that could walk, float, flutter, slither or ooze its way around a room, and adapt whatever it is you want to say to fit what your audience expects to hear.

It's the speed of group conversation that's hardest for me to deal with, for a lot of reasons. One reason is that, since I don't hear tones of voice or anything "meta" to the actual words being spoken (I can infer sarcasm from context --- say, if I know the person and they are saying something diametrically opposed to what I know they believe --- but my first instinct is always to take things literally), I cannot tell the difference between a silence that signifies that someone has finished speaking, and a pause in the middle of a block of speech. I distinguish them by waiting to see if the person resumes speaking; if they never do, I decide that the way is clear for me to respond.

Of course, in all the time it takes me to do this, someone else has already perceived the opening and begun to speak.

The other big problem I have with speaking, and responding to other people's speech, is that I don't think in words. It can take me a very long time to convert what's going on in my head --- which is sometimes a single still image, sometimes a slideshow of images, sometimes just a jumble of colors and shapes, moving and changing, and sometimes looks like nothing at all, even to me on the inside --- into coherent, grammatically-correct, meaningful language. It is somewhat easier to effect this transformation in writing, where what I have already written stays there for me to read, to orient myself and build on, while in speech all the progress I've made evaporates into the air, leaving me nothing to work with. Most importantly, though, in writing I have the luxury of waiting as long as it takes for my thoughts to solidify into nameable concepts.

Time is not on my side when I'm trying to participate in a group discussion. I can't wait for my thoughts to reveal themselves to me in communicable form, but neither can I describe what I see as it appears to me; most of the things I see elude description, or, if they can be described, defy interpretation. The thing I can do earliest is perceive an absence; sense something that is not being addressed. I can't always see what's missing, but I can usually tell that something is.

When that happens, I've learned to tell people to wait.

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Other Autistics who are Speaking today:

Bev at Square 8 says, "Squawk?"

Corina Becker has posted a roundup of her own past writings about autism

The Untoward Lady writes about being autistic and in love

Amanda Forest Vivian has two posts, one about how 1) passing as non-disabled can be a mixed blessing and 2) therapies that are primarily geared toward turning non-passing people into passing people are misguided; and one about "Regular Person Listening Day"

Kat Bjornstad has a link roundup, and a discussion of her experiences starting a blog and running an Autistics Speaking Day Facebook event

Rachel Cohen-Rottenberg at Journeys with Autism speaks her mind, and also speaks from her heart

Clarissa wants to know, "How Does Silence Support Autism?"

Astrid van Woerkom sometimes loses the ability to speak

Savannah Logsdon-Breakstone has reposted several of her poems --- "Articulate", "Analogy > Simile > Metaphor and Me", "Feet", "Poetry and the Vision of Thought", "To Inspiration", and "Allied, Unallied, Re-Allied" --- and an "accessible interpretation" of her poem "To Inspiration"

Leah Jane at The Quixotic Autistic talks about a project she's been working on with her local autism club

Clay Adams reposts an essay by Ari Ne'eman

(That's not all, not by a longshot. Kat's link roundup has more, and Sunday Stilwell at Adventures in Extreme Parenthood and Kim Wombles and Kathleen Leopold at the Autism Blogs Directory all have link roundups of their own)