CHD9 — 346 ClinVar variants

All ClinVar germline CHD9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 164 flagged for review →

1 Benign · 12 Likely benign · 333 Uncertain significance

Full CHD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 164

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors lean, ClinVar uncertain 149

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 15

The independent predictors disagree with each other — read with care.

All CHD9 variants

Benign 1

p.Met2710Val Single submitter

Likely benign 12

c.2878-8A>T Single submitter
c.4968-4A>T Single submitter
p.Arg836His Single submitter
p.Asn2399Ser Single submitter
p.Gly595= Single submitter
p.Lys1738Arg Single submitter
p.Phe783Leu Single submitter ⚠
p.Pro574= Single submitter
p.Ser442= Single submitter
p.Thr1389= Single submitter
p.Thr1565= Single submitter
p.Thr2182Ser Single submitter

Uncertain significance 333

Showing the top 300 by review status; the full set is in the sitemap.

c.6620-2A>C Single submitter
p.Ala1363Thr Single submitter ⚠
p.Ala1408Val Single submitter ⚠
p.Ala1537Thr Single submitter
p.Ala167Val Single submitter
p.Ala1724Gly Single submitter
p.Ala1742Val Single submitter
p.Ala1938Thr Single submitter ⚠
p.Ala2007Val Single submitter ⚠
p.Ala2214Thr Single submitter
p.Ala2221Thr Single submitter
p.Ala2289Pro Single submitter ⚠
p.Ala2289Val Single submitter ⚠
p.Ala2596Pro Single submitter
p.Ala2641Asp Single submitter
p.Ala2785Thr Single submitter
p.Ala291Ser Single submitter ⚠
p.Ala294Gly Single submitter ⚠
p.Ala294Pro Single submitter
p.Ala294Val Single submitter ⚠
p.Ala460Val Single submitter ⚠
p.Ala646Ser Single submitter ⚠
p.Ala646Val Single submitter ⚠
p.Ala819Gly Single submitter ⚠
p.Ala921Thr Single submitter ⚠
p.Ala921Val Single submitter
p.Arg1209Cys Single submitter ⚠
p.Arg1309Cys Single submitter
p.Arg1385His Single submitter ⚠
p.Arg1397Cys Single submitter
p.Arg1481Gln Single submitter
p.Arg1486Cys Single submitter
p.Arg1486His Single submitter
p.Arg1509Ter Single submitter
p.Arg1518His Single submitter
p.Arg1544Gln Single submitter
p.Arg1566Leu Single submitter
p.Arg1603Gln Single submitter
p.Arg178Cys Single submitter
p.Arg178His Single submitter ⚠
p.Arg1895Gln Single submitter ⚠
p.Arg1895Trp Single submitter ⚠
p.Arg1899Cys Single submitter
p.Arg1947Cys Single submitter
p.Arg1947His Single submitter
p.Arg1981Gln Single submitter
p.Arg2103His Single submitter ⚠
p.Arg2206Gln Single submitter ⚠
p.Arg2262His Single submitter ⚠
p.Arg2385Gln Single submitter
p.Arg2432Leu Single submitter ⚠
p.Arg2536Lys Single submitter
p.Arg2545Lys Single submitter
p.Arg2616Cys Single submitter
p.Arg2632Lys Single submitter
p.Arg2633Gln Single submitter
p.Arg447Gln Single submitter ⚠
p.Arg461Gln Single submitter ⚠
p.Arg528Cys Single submitter
p.Arg540Cys Single submitter ⚠
p.Arg543Cys Single submitter ⚠
p.Arg835Gly Single submitter ⚠
p.Arg839Cys Single submitter ⚠
p.Arg839His Single submitter ⚠
p.Arg961Cys Single submitter
p.Arg961His Single submitter ⚠
p.Arg992Gln Single submitter ⚠
p.Asn112Ser Single submitter
p.Asn1488Ser Single submitter ⚠
p.Asn1796Asp Single submitter ⚠
p.Asn1798Ser Single submitter ⚠
p.Asn2051Ser Single submitter ⚠
p.Asn236Asp Single submitter
p.Asn2447Ser Single submitter
p.Asn2548Ser Single submitter ⚠
p.Asn2656Ser Single submitter ⚠
p.Asn2661Ile Single submitter ⚠
p.Asn2661Ser Single submitter
p.Asn299Asp Single submitter
p.Asn327Ser Single submitter
p.Asn375Ser Single submitter ⚠
p.Asn477Ser Single submitter ⚠
p.Asn527Asp Single submitter ⚠
p.Asn858Ser Single submitter
p.Asp1248Gly Single submitter
p.Asp1277Gly Single submitter ⚠
p.Asp1318Asn Single submitter
p.Asp1318Gly Single submitter ⚠
p.Asp1354Val Single submitter ⚠
p.Asp1418Asn Single submitter
p.Asp1595Gly Single submitter ⚠
p.Asp1762Gly Single submitter ⚠
p.Asp1764Gly Single submitter
p.Asp1771Tyr Single submitter ⚠
p.Asp1881Asn Single submitter ⚠
p.Asp1881Gly Single submitter
p.Asp2228Gly Single submitter
p.Asp2232Asn Single submitter neurodevelopmental disorder
p.Asp2502Asn Single submitter ⚠
p.Asp2502Glu Single submitter
p.Asp2826Ala Single submitter
p.Asp363Ala Single submitter ⚠
p.Asp366Gly Single submitter
p.Asp376His Single submitter
p.Asp475Gly Single submitter ⚠
p.Asp492Asn Single submitter ⚠
p.Asp578Gly Single submitter ⚠
p.Asp613Gly Single submitter
p.Asp648Gly Single submitter ⚠
p.Asp648Val Single submitter ⚠
p.Asp815Asn Single submitter
p.Asp815Val Single submitter ⚠
p.Cys2156Phe Single submitter
p.Cys2156Trp Single submitter
p.Cys2171Tyr Single submitter
p.Cys262Ser Single submitter
p.Cys480Arg Single submitter ⚠
p.Cys993Ser Single submitter ⚠
p.Gln1289Glu Single submitter ⚠
p.Gln1564Lys Single submitter ⚠
p.Gln1647Ter Single submitter
p.Gln171Lys Single submitter
p.Gln1805Arg Single submitter ⚠
p.Gln1937Arg Single submitter
p.Gln2057His Single submitter ⚠
p.Gln2362Glu Single submitter
p.Gln268Glu Single submitter
p.Gln269Glu Single submitter
p.Gln288Arg Single submitter
p.Gln455His Single submitter ⚠
p.Gln501Lys Single submitter ⚠
p.Gln70Pro Single submitter ⚠
p.Gln828Arg Single submitter
p.Glu1084Gln Single submitter
p.Glu1099Val Single submitter ⚠
p.Glu1139Lys Single submitter ⚠
p.Glu1393Gly Single submitter ⚠
p.Glu1664Gly Single submitter
p.Glu1962Asp Single submitter
p.Glu2139Ala Single submitter ⚠
p.Glu2202Ala Single submitter
p.Glu2352Gln Single submitter
p.Glu2394Asp Single submitter
p.Glu2439Asp Single submitter
p.Glu2521Lys Single submitter
p.Glu2611Ala Single submitter
p.Glu2749Asp Single submitter
p.Glu2853Lys Single submitter
p.Glu510Gly Single submitter ⚠
p.Gly1691Ala Single submitter ⚠
p.Gly1973Asp Single submitter ⚠
p.Gly1978Arg Single submitter ⚠
p.Gly2090Arg Single submitter ⚠
p.Gly2372Arg Single submitter ⚠
p.Gly2375Ser Single submitter
p.Gly2662Ala Single submitter
p.Gly2697Ser Single submitter ⚠
p.Gly316Arg Single submitter ⚠
p.Gly316Glu Single submitter
p.Gly372Val Single submitter
p.Gly403Glu Single submitter
p.Gly424Arg Single submitter
p.Gly595Arg Single submitter
p.Gly651Glu Single submitter ⚠
p.Gly87Ser Single submitter ⚠
p.His148Tyr Single submitter
p.His1542Arg Single submitter ⚠
p.His1667Tyr Single submitter ⚠
p.His2327Pro Single submitter ⚠
p.His2327Tyr Single submitter ⚠
p.His358Tyr Single submitter
p.His377Arg Single submitter
p.His434Arg Single submitter ⚠
p.His55Arg Single submitter ⚠
p.Ile1097Val Single submitter
p.Ile1219Leu Single submitter ⚠
p.Ile1274Val Single submitter
p.Ile1364Val Single submitter
p.Ile1434Thr Single submitter ⚠
p.Ile1972Thr Single submitter
p.Ile2404Thr Single submitter ⚠
p.Ile2490Thr Single submitter
p.Ile2816Val Single submitter ⚠
p.Ile281Met Single submitter ⚠
p.Ile317Val Single submitter ⚠
p.Ile50Val Single submitter ⚠
p.Ile529Met Single submitter ⚠
p.Ile529Val Single submitter ⚠
p.Ile615Val Single submitter ⚠
p.Ile920Val Single submitter
p.Ile962Val Single submitter ⚠
p.Ile963Leu Single submitter
p.Leu1036Val Single submitter ⚠
p.Leu1090fs Single submitter
p.Leu1133Phe Single submitter
p.Leu1224Ser Single submitter
p.Leu1224Val Single submitter
p.Leu1322Phe Single submitter
p.Leu2415Phe Single submitter
p.Leu2492Arg Single submitter
p.Leu414Phe Single submitter
p.Leu415Arg Single submitter
p.Leu597Val Single submitter ⚠
p.Leu917Pro Single submitter ⚠
p.Leu980Phe Single submitter ⚠
p.Lys1123Glu Single submitter ⚠
p.Lys1156fs Single submitter
p.Lys1156Gln Single submitter
p.Lys1461Glu Single submitter
p.Lys1604Arg Single submitter
p.Lys2097Arg Single submitter ⚠
p.Lys2402Asn Single submitter
p.Lys2436Arg Single submitter ⚠
p.Lys2640Thr Single submitter
p.Lys2830Arg Single submitter ⚠
p.Lys489Asn Single submitter
p.Lys512Gln Single submitter ⚠
p.Lys589Arg Single submitter ⚠
p.Lys603Arg Single submitter
p.Lys604Arg Single submitter
p.Met1138Val Single submitter ⚠
p.Met1365Thr Single submitter ⚠
p.Met150Val Single submitter ⚠
p.Met228Ile Single submitter ⚠
p.Met2727Val Single submitter
p.Met371Thr Single submitter
p.Met451Val Single submitter ⚠
p.Met5Leu Single submitter ⚠
p.Met6Ile Single submitter
p.Met947Thr Single submitter
p.Met978Val Single submitter
p.Phe1048Cys Single submitter ⚠
p.Phe1808Ser Single submitter
p.Phe2295Leu Single submitter
p.Phe241Leu Single submitter
p.Phe311Ser Single submitter ⚠
p.Phe717Tyr Single submitter ⚠
p.Phe760Leu Single submitter
p.Phe898Leu Single submitter ⚠
p.Phe9Ser Single submitter ⚠
p.Pro111Ser Single submitter ⚠
p.Pro1247Leu Single submitter ⚠
p.Pro1478Leu Single submitter
p.Pro1607Leu Single submitter ⚠
p.Pro1806Leu Single submitter
p.Pro1965Arg Single submitter ⚠
p.Pro2027His Single submitter
p.Pro2077Arg Single submitter ⚠
p.Pro2111Arg Single submitter
p.Pro2121Arg Single submitter ⚠
p.Pro214Ser Single submitter ⚠
p.Pro2369Leu Single submitter
p.Pro2426Ser Single submitter
p.Pro2470Ala Single submitter
p.Pro2517Leu Single submitter ⚠
p.Pro257Arg Single submitter
p.Pro257Leu Single submitter
p.Pro2712Ser Single submitter ⚠
p.Pro2774Leu Single submitter
p.Pro2804Thr Single submitter ⚠
p.Pro2860Leu Single submitter ⚠
p.Pro30Gln Single submitter ⚠
p.Pro32Leu Single submitter ⚠
p.Pro345Thr Single submitter
p.Pro406Arg Single submitter
p.Pro485Leu Single submitter ⚠
p.Pro555Ser Single submitter
p.Pro684Leu Single submitter
p.Pro707Ser Single submitter ⚠
p.Pro767Gln Single submitter
p.Pro792Thr Single submitter ⚠
p.Pro841His Single submitter
p.Ser122Arg Single submitter
p.Ser139Cys Single submitter
p.Ser1779Ala Single submitter
p.Ser179Leu Single submitter
p.Ser2066Ala Single submitter ⚠
p.Ser2142Tyr Single submitter
p.Ser220Pro Single submitter ⚠
p.Ser2314Arg Single submitter
p.Ser2314Asn Single submitter ⚠
p.Ser2393Leu Single submitter
p.Ser2777Phe Single submitter
p.Ser2820Phe Single submitter
p.Ser2836Leu Single submitter ⚠
p.Ser2867Thr Single submitter
p.Ser2893Cys Single submitter
p.Ser2893Tyr Single submitter
p.Ser295Ala Single submitter ⚠
p.Ser331Pro Single submitter
p.Ser350Asn Single submitter
p.Ser367Leu Single submitter
p.Ser385Cys Single submitter
p.Ser442Leu Single submitter ⚠
p.Ser487Tyr Single submitter ⚠
p.Ser550Gly Single submitter ⚠
p.Ser611Pro Single submitter
p.Ser616Pro Single submitter
p.Ser631Phe Single submitter ⚠
p.Thr1136Ala Single submitter ⚠