Research Article

Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan

Table 2

Characteristics of rare inherited variants.

No.NameSIFT/PolyPhenClinical significance (last reviewed)dbSNP IDGMAFTypeFamily No.

1NM_000055.2 (BCHE):c.293A>G (p.Asp98Gly)Deleterious (0.01)/possibly damaging (0.511)Pathogenic/likely pathogenic (last reviewed: May 29, 2020)rs17998070.00599 (C)Missense variant1
2NM_019000.4 (RETREG1):c.503C>G (p.Ser168Ter)-/-Pathogenic (last reviewed: Jun 3, 2020)rs1378527390.00020 (A)Stop gained1; 2; 3; 4
3NM_004646.3 (NPHS1):c.2869G>A (p.Val957Met)Deleterious (0.02)/probably damaging (0.995)Likely pathogenic (last reviewed: May 25, 2018)rs1148491390.00280 (G)Missense variant2
4NM_017882.3 (CLN6):c.307C>T (p.Arg103Trp)Deleterious (0)/probably damaging (0.999)Conflicting interpretations of pathogenicity (last reviewed: Sep 21, 2020)rs2010954120.00020 (A)Missense variant4
5NM_000256.3 (MYBPC3):c.649A>G (p.Ser217Gly)Deleterious (0.01)/possibly damaging (0.541)Conflicting interpretations of pathogenicity (last reviewed: Sep 20, 2021)rs1387538700.00180 (C)Missense variant4
6NM_000369.5 (TSHR):c.1349G>A (p.Arg450His)Deleterious (0)/probably damaging (0.999)Conflicting interpretations of pathogenicity (last reviewed: Sep 1, 2021)rs1892618580.00020 (A)Missense variant4
7NM_003122.4 (SPINK1):c.194+2T>C-/-Conflicting interpretations of pathogenicity (last reviewed: Oct 7, 2020)rs1489543870.00080 (G)Splice donor variant3
8NM_000036.3 (AMPD1):c.860A>T (p.Lys287Ile)Deleterious (0)/probably damaging (1)Conflicting interpretations of pathogenicity (last reviewed: Oct 31, 2018)rs345261990.01098 (A)Missense variant1; 4
9NM_020631.5 (PLEKHG5):c.2485G>T (p.Asp829Tyr)Deleterious (0)/possibly damaging (0.876)Conflicting interpretations of pathogenicity (last reviewed: Oct 29, 2020)rs2001625210.00020 (A)Missense variant1
10NM_000540.3 (RYR1):c.9713A>G (p.Glu3238Gly)Deleterious (0.01)/possibly damaging (0.503)Conflicting interpretations of pathogenicity (last reviewed: Nov 3, 2020)rs2009506730.00020 (G)Missense variant4
11NM_001849.4 (COL6A2):c.2795C>TTolerated (0.23)/benign (0.041)Conflicting interpretations of pathogenicity (last reviewed: Nov 27, 2020)rs1177258250.00160 (T)Missense variant4
12NM_000335.5 (SCN5A):c.4821C>T (p.Leu1607=)-/-Conflicting interpretations of pathogenicity (last reviewed: Nov 25, 2020)rs454370990.00100 (A)Synonymous variant3; 4
13NM_001267550.2(TTN):c.102595A>G (p.Ile34199Val)-/benign (0.151)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs563472480.00599 (C)Missense variant3
14NM_001267550.2(TTN):c.101891G>A (p.Arg33964His)-/benign (0.018)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs556695530.00599 (T)Missense variant3
15NM_001267550.2(TTN):c.95297C>T (p.Ser31766Phe)-/probably damaging (0.998)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs1914848940.00599 (A)Missense variant3
16NM_001267550.2(TTN):c.90536G>A (p.Arg30179His)-/probably damaging (0.998)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs1495673780.00619 (T)Missense variant3
17NM_001267550.2(TTN):c.82560C>A (p.Asn27520Lys)-/probably damaging (0.997)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs562648400.00579 (T)Missense variant3
18NM_001267550.2(TTN):c.49919G>C (p.Ser16640Thr)-/probably damaging (0.991)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs556630500.00599 (G)Missense variant3
19NM_001267550.2(TTN):c.47545C>A (p.Pro15849Thr)-/benign (0.15)Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs1461814770.00599 (T)Missense variant3
20NM_001267550.2(TTN):c.1137A>G (p.Arg379=)-/-Conflicting interpretations of pathogenicity (last reviewed: Nov 21, 2020)rs559725470.00599 (C)Synonymous variant3
21NM_172364.5(CACNA2D4):c.2120G>A (p.Arg707His)Tolerated (0.4)/possibly damaging (0.795)Conflicting interpretations of pathogenicity (last reviewed: Nov 18, 2020)rs760649260.00719 (T)Missense variant3
22NM_018100.4(EFHC1):c.685T>C (p.Phe229Leu)Tolerated (0.12)/benign (0.039)Conflicting interpretations of pathogenicity (last reviewed: May 5, 2021)rs1378527760.00180 (C)Missense variant3
23NM_003126.4(SPTA1):c.6421C>T (p.Arg2141Trp)Deleterious (0.01)/probably damaging (1)Conflicting interpretations of pathogenicity (last reviewed: May 30, 2019)rs412735190.00160 (A)Missense variant4
24NM_001271208.2(NEB):c.571G>C (p.Glu191Gln)Deleterious (0.09)/probably damaging (0.999)Conflicting interpretations of pathogenicity (last reviewed: May 18, 2021)rs356869680.00719 (G)Missense variant3
25NM_000784.4(CYP27A1):c.1151C>T (p.Pro384Leu)Deleterious (0)/probably damaging (0.991)Conflicting interpretations of pathogenicity (last reviewed: May 18, 2021)rs412726870.00859 (T)Missense variant3
26NM_000237.3(LPL):c.953A>G (p.Asn318Ser)Tolerated (0.24)/benign (0.137)Conflicting interpretations of pathogenicity (last reviewed: May 18, 2021)rs2680.00519 (G)Missense variant1
27NM_000243.2(MEFV):c.1772T>C (p.Ile591Thr)Tolerated (0.55)/benign (0)Conflicting interpretations of pathogenicity (last reviewed: May 18, 2021)rs114660450.00439 (G)Missense variant1
28NM_001370466.1(NOD2):c.332G>A (p.Arg111Gln)Deleterious (0)/benign (0.116)Conflicting interpretations of pathogenicity (last reviewed: May 14, 2018)rs1048954560.00020 (A)Missense variant4
29NM_014588.5(VSX1):c.479G>A (p.Gly160Asp)Tolerated (0.3)/benign (0.156)Conflicting interpretations of pathogenicity (last reviewed: Mar 6, 2018)rs743154330.00260 (A)Missense variant4
30NM_020812.4(DOCK6):c.4862T>C (p.Val1621Ala)Deleterious (0)/benign (0.161)Conflicting interpretations of pathogenicity (last reviewed: Mar 19, 2021)rs2017388180.00120 (G)Missense variant2
31NM_000136.3(FANCC):c.77C>T (p.Ser26Phe)Deleterious (0)/probably damaging (0.948)Conflicting interpretations of pathogenicity (last reviewed: Jun 1, 2021)rs18003610.00260 (A)Missense variant2
32NM_006432.4(NPC2):c.441+1G>A-/-Conflicting interpretations of pathogenicity (last reviewed: Jun 1, 2021)rs1401300280.00100 (T)Splice donor variant3; 4
33NM_000492.4(CFTR):c.1584G>A (p.Glu528=)-/-Conflicting interpretations of pathogenicity (last reviewed: Jul 22, 2021)rs18000950.01058 (A)Synonymous variant4
34NM_001267550.2(TTN):c.14698G>A (p.Ala4900Thr)-/probably damaging (0.926)Conflicting interpretations of pathogenicity (last reviewed: Jul 1, 2021)rs726489230.00180 (T)Missense variant2
35NM_001079802.2(FKTN):c.1297A>G (p.Thr433Ala)Tolerated (0.52)/benign (0.005)Conflicting interpretations of pathogenicity (last reviewed: Jul 1, 2021)rs1419184320.00100 (G)Missense variant4
36NM_022168.4(IFIH1):c.1879G>T (p.Glu627Ter)-/-Conflicting interpretations of pathogenicity (last reviewed: Jan 1, 2021)rs357446050.00140 (A)Stop gained1
37NM_001267550.2(TTN):c.48727C>T (p.Pro16243Ser)-/benign (0.068)Conflicting interpretations of pathogenicity (last reviewed: Feb 4, 2021)rs726772420.00160 (A)Missense variant2
38NM_000548.5(TSC2):c.1939G>A (p.Asp647Asn)Deleterious (0.01)/probably damaging (0.995)Conflicting interpretations of pathogenicity (last reviewed: Dec 7, 2020)rs455093920.00040 (A)Missense variant2
39NM_000371.4(TTR):c.417G>A (p.Thr139=)-/-Conflicting interpretations of pathogenicity (last reviewed: Dec 7, 2020)rs22763820.00359 (A)Synonymous variant1
40NM_001267550.2(TTN):c.65775C>T (p.Ser21925=)-/-Conflicting interpretations of pathogenicity (last reviewed: Dec 6, 2020)rs726468670.00160 (A)Synonymous variant2
41NM_000527.5(LDLR):c.148G>T (p.Ala50Ser)Tolerated (0.33)/benign (0.169)Conflicting interpretations of pathogenicity (last reviewed: Dec 6, 2020)rs1378539600.00060 (A)Missense variant1
42NM_012472.6(DNAAF11):c.1391C>T (p.Pro464Leu)Deleterious (0)/probably damaging [1]Conflicting interpretations of pathogenicity (last reviewed: Dec 31, 2019)rs1391314850.00080 (A)Missense variant1
43NM_005634.2(SOX3):c.157G>C (p.Val53Leu)Tolerated (0.11)/benign (0.001)Conflicting interpretations of pathogenicity (last reviewed: Dec 31, 2019)rs2003611280.00265 (G)Missense variant4
44NM_000065.4(C6):c.2381+2T>C-/-Conflicting interpretations of pathogenicity (last reviewed: Dec 22, 2017)rs762029090.00120 (G)Splice donor variant1
45NM_001037.5(SCN1B):c.28G>A (p.Gly10Ser)Tolerated (0.4)/possibly damaging (0.862)Conflicting interpretations of pathogenicity (last reviewed: Dec 2, 2020)rs725520270.00319 (A)Missense variant2
46NM_006214.4(PHYH):c.734G>A (p.Arg245Gln)Deleterious (0.01)/benign (0.393)Conflicting interpretations of pathogenicity (last reviewed: Aug 6, 2020)rs626199190.00539 (T)Missense variant4
47NM_201596.3(CACNB2):c.1816C>T (p.Arg606Trp)Deleterious (0.03)/probably damaging (0.928)Conflicting interpretations of pathogenicity (last reviewed: Aug 6, 2020)rs617339680.00439 (G)Missense variant4
48NM_000275.3(OCA2):c.1441G>A (p.Ala481Thr)Tolerated (0.09)/possibly damaging (0.621)Conflicting interpretations of pathogenicity (last reviewed: Apr 20, 2021)rs746533300.00799 (T)Missense variant1;3
49NM_025216.3(WNT10A):c.511C>T (p.Arg171Cys)Deleterious (0)/probably damaging (0.93)Conflicting interpretations of pathogenicity (last reviewed: Apr 13, 2021)rs1169985550.00319 (T)Missense variant1; 2;3; 4
50NM_001110792.2(MECP2):c.638C>T (p.Ala213Val)Tolerated (0.07)/benign (0)Benign/likely benign (last reviewed: Dec 31, 2019)rs617483810.00477 (A)Missense variant4