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I am reading a journal paper about the relationship between the protein NCAM2 and autism, and I have come across the following statement:

We report three patients affected with neurodevelopmental disorders and harbouring 21q21 deletions involving NCAM2 gene.

I am not sure what a 21q21 deletion is. I have read that 21q refers to long arm of chromosome 21, and that 21q21 refers to position 21 on the long arm of chromosome 21. However would a 21q21 deletion, refer to this whole section of the chromosome being missing, with this section including the NCAM2 gene? Any insights are appreciated.

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Two likely scenarios.

Interstitial deletion. More likely. Where just a small internal part of the chromosome is missing. This is like pressing "delete" for a while in the middle of a text document.

Deletions from the end of the chromosome to some point.

Chromosome 21 is the smallest, and people survive having the whole p side of the chromosome missing, even all the way down into band 21 on the q side.

There are more recent articles than the one you saw, look on google scholar for ncam2 deletion and sort by date.

Wikipedia article.

https://en.wikipedia.org/wiki/Chromosome_21

This document below mentions specific cases of (severe) 21q21 deletions (page 15).

https://www.rarechromo.org/media/information/Chromosome%2021/21q%20deletions%20FTNW.pdf

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I would suggest looking more into karyotype nomenclature; it is admittedly a bit odd. Here is one related question/answer that puts it in context.

I haven't looked at the paper in detail but generally what it means is that there is some cytologically relevant big chunk of chromosome that is missing that roughly overlaps with the chunk of chromosome that we find at band 21 of chromosome 21 (not position 21). Note that these cytobands/karyotype/G bands visible in a chromosome spread under a microscope, so these are quite large deletions.

Looking at the paper methods, it is clear that in 2/3 cases they confirmed the deletions by looking at karyotype data (FISH/chromosome spreads):

For Case 2, CNV confirmation and parental studies were performed by metaphasic and interphasic FISH on leucocytes using BAC RP11-43A6 (chr21:18,414,905e18,567,253, hg19 build). For Case 3, CNV confirmation was performed by G-banded karyotype. Parental studies were not available.

The terminology is quite outdated now as usually we are looking at sequence data these days, which has much higher resolution, but a lot of the stereotypical chromosomal abnormalities still carry these confusing names. And seeing it on a chromosome under a microscope is still the gold standard for these large chromosomal events.

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