Table 2 Candidate variants: Genomic coordinates are given relative to GRCh37/hg19 build. gnomAD minor allele frequency (MAF) v2.1.1 is provided, with number of homozygotes or hemizygotes for X-linked (XL) genes given in parentheses. * indicates the variant is located within an HBD block (in a multiplex family). ClinVar reports were identified from other studies or diagnostic clinics for TTC19 (recorded as pathogenic and likely pathogenic), GML (benign), and POLR3G (variant of uncertain significance) (accessed 19 Jan 2024).
From: Biallelic variants identified in 36 Pakistani families and trios with autism spectrum disorder
Family ID | Sex | Chromosome | Gene | mRNA variant | Protein variant | Mutation type | Mutation effect | gnomAD MAF all | gnomAD MAF S. Asian |
|---|---|---|---|---|---|---|---|---|---|
PKASD-14 | M | 3:36905962T > C* | TRANK1 | NM_001329998.2:c.1088A > G | p.Asn363Ser | Homo | Missense | 2.99E−05 (0) | 2.00E−04 (0) |
3:36931409T > C* | TRANK1 | NM_001329998.2:c.818A > G | p.Glu273Gly | Homo | Missense | 7.62E−04 (0) | 4.84E−04 (0) | ||
PKASD-18 | M | X:18646620A > G | CDKL5 | NM_003159.3:c.2626A > G | p.Ile876Val | XL | Missense | 0 | 0 |
PKASD-19 | M | X:48762117C > G | SLC35A2 | NM_001042498.3:c.1069G > C | p.Gly357Arg | XL | Missense | 1.1E−05 (1) | 5.304E−05 (1) |
PKASD-26 | M | 17:15909789C > T | TTC19a | NM_017775.4:c.583C > T | p.Gln195* | Homo | Stop gain | 3.18E−05 (0) | 3.266E−05 (0) |
6:87971373G > A* | ZNF292 | NM_015021.3:c.8026G > A | p.Asp2676Asn | Homo | Missense | 3.891E−04 (0) | 3.486E−03 (0) | ||
8:117767987G > C* | EIF3H | NM_003756.3:c.50C > G | p.Ser17Cys | Homo | Missense | 7.562E−05 (0) | 6.206E−04 (0) | ||
8:143921881A > G* | GMLb | NM_002066.3:c.28A > G | p.Met10Val | Homo | Missense | 4.95E−05 (0) | 1.96E−04 (0) | ||
PKASD-32 | M | 15:56207541C > T | NEDD4 | NM_001284338.2:c.1489G > A | p.Asp497Asn | De novo | Missense | 0 | 0 |
PKASD-37 | M | 3:129147293C > G | EFCAB12 | NM_207307.3:c.39G > C | p.Leu13Phe | Homo | Missense | 1.871E−4 (0) | 1.489E−3 (0) |
X:153070213G > A | PDZD4 | NM_001303512.2:c.923C > T | p.Pro308Leu | XL | Missense | 5.5E−06 (0) | 0 | ||
11:72410069C > T | ARAP1 | NM_001040118.3:c.2522G > A | p.Trp841* | De novo | Stop gain | 0 | 0 | ||
PKASD-39 | M | 1:34082538C > T | CSMD2 | NM_001281956.2:c.5984G > A | p.Arg1995Gln | De novo | Missense | 0 | 0 |
PKASD-47 | M | 2:27259973G > A | TMEM214 | NM_017727.5:c.937G > A | p.Gly313Ser | Homo | Missense | 1.21E−04 (0) | 8.496E−04 (0) |
5:89781487C > A | POLR3Gc | NM_006467.3:c.103C > A | p.Pro35Thr | Homo | Missense | 1.429E−04 (0) | 2.973E−04 (0) | ||
5:109973924T > C | TMEM232 | NM_001039763.4:c.476A > G | p.Tyr159Cys | Homo | Missense | 0 | 0 |
