WASHC4 — 248 ClinVar variants

All ClinVar germline WASHC4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 155 flagged for review →

3 Pathogenic · 11 Likely pathogenic · 8 Conflicting · 10 Benign · 5 Benign/Likely benign · 44 Likely benign · 167 Uncertain significance

Full WASHC4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 155

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

WASHC4 p.Lys1079Arg Likely pathogenic Single submitter
intellectual disability, autosomal recessive 43

Predictors agree, ClinVar conflicts 6

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

WASHC4 p.Ala1096Thr Conflicting Single submitter
WASHC4 p.Arg293Gln Conflicting Single submitter
Inborn genetic diseases
WASHC4 p.Arg721His Conflicting Single submitter
WASHC4 p.Asn60Ser Conflicting Single submitter
WASHC4 p.His503Arg Conflicting Single submitter
intellectual disability, autosomal recessive 43
WASHC4 p.His822Arg Conflicting Single submitter

Predictors lean, ClinVar uncertain 112

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

Predictors split 36

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

All WASHC4 variants

Pathogenic 3

p.Asp1048Gly No assertion criteria intellectual disability, autosomal recessive 43
p.Gln442Ter No assertion criteria intellectual disability, autosomal recessive 43
p.Pro1019Arg No assertion criteria intellectual disability, autosomal recessive 43

Likely pathogenic 11

c.1038+1G>T Single submitter intellectual disability, autosomal recessive 43
p.Arg556Ter Single submitter intellectual disability, autosomal recessive 43
p.Arg596Ter Single submitter intellectual disability, autosomal recessive 43
p.Arg871Ter Single submitter intellectual disability, autosomal recessive 43
p.Arg982Ter Single submitter intellectual disability, autosomal recessive 43
p.Gln506fs Single submitter
p.Lys1079Arg Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Met458fs Single submitter intellectual disability, autosomal recessive 43
p.Phe853fs Single submitter intellectual disability, autosomal recessive 43
p.Ser712fs Single submitter intellectual disability, autosomal recessive 43
p.Tyr405Ter Single submitter

Conflicting classifications of pathogenicity 8

p.Ala1096Thr Single submitter ⚠
p.Arg1112Ter Single submitter intellectual disability, autosomal recessive 43
p.Arg293Gln Single submitter Inborn genetic diseases ⚠
p.Arg721His Single submitter ⚠
p.Asn60Ser Single submitter ⚠
p.His503Arg Single submitter intellectual disability, autosomal recessive 43 ⚠
p.His822Arg Single submitter ⚠
p.Tyr1014Cys Single submitter intellectual disability ⚠

Benign 10

p.Glu592= Multiple submitters
p.Leu1103= Multiple submitters
p.Leu547= Multiple submitters
p.Leu956= Multiple submitters
p.Thr39= Multiple submitters
p.Val901Ile Multiple submitters intellectual disability, autosomal recessive 43
c.201+8T>G Single submitter
c.2409+30dup Single submitter
p.Thr599Ser Single submitter
p.Tyr38His No assertion criteria WASHC4-related disorder ⚠

Benign/Likely benign 5

p.Ala1096= Multiple submitters
p.Gln855= Multiple submitters
p.Leu1102= Multiple submitters
p.Leu144= Multiple submitters
p.Met128Ile Multiple submitters

Likely benign 44

c.3158-8G>T Multiple submitters
p.Ala289Val Multiple submitters
p.Asp47= Multiple submitters
p.Gly900= Multiple submitters
c.1560+7A>T Single submitter
c.2180-4G>T Single submitter
c.2180-5G>T Single submitter
c.2334+23dup Single submitter
c.2409+29_2409+30dup Single submitter
c.2410-7A>G Single submitter
c.2759-12G>A Single submitter
c.2913-5T>C Single submitter
c.321+14T>C Single submitter
c.3455-7C>T Single submitter
c.519-7A>G Single submitter
c.561+12T>C Single submitter
c.910+13G>A Single submitter
p.Ala985= Single submitter
p.Arg1085= Single submitter
p.Arg222= Single submitter
p.Arg610= Single submitter
p.Arg648= Single submitter
p.Cys133= Single submitter
p.Glu487= Single submitter
p.Glu989= Single submitter
p.Gly905= Single submitter
p.Ile332Val Single submitter
p.Ile343= Single submitter
p.Ile365= Single submitter
p.Leu1113= Single submitter
p.Leu1123= Single submitter
p.Leu223= Single submitter
p.Lys1059= Single submitter
p.Phe710= Single submitter
p.Phe805= Single submitter
p.Pro467= Single submitter
p.Ser410= Single submitter
p.Ser525= Single submitter
p.Thr837= Single submitter
p.Tyr155= Single submitter
p.Val278= Single submitter
p.Val323Leu Single submitter
p.Leu482Phe No assertion criteria WASHC4-related disorder
p.Lys1111= No assertion criteria WASHC4-related disorder

Uncertain significance 167

p.Arg556Gln Multiple submitters ⚠
p.Arg638Cys Multiple submitters ⚠
p.Arg638His Multiple submitters ⚠
p.Arg726Trp Multiple submitters ⚠
p.Arg808Gln Multiple submitters intellectual disability, autosomal recessive 43 ⚠
p.Asn720Ser Multiple submitters ⚠
p.Asn893Ser Multiple submitters ⚠
p.Asp1062Ala Multiple submitters ⚠
p.Asp208Gly Multiple submitters ⚠
p.Leu508Phe Multiple submitters ⚠
p.Lys214Arg Multiple submitters intellectual disability, autosomal recessive 43 ⚠
p.Ser52Ala Multiple submitters intellectual disability, autosomal recessive 43 ⚠
p.Val957Leu Multiple submitters ⚠
c.2011-1G>A Single submitter
c.2650-3T>G Single submitter
c.2759-1539del Single submitter intellectual disability, autosomal recessive 43
c.3060+1G>C Single submitter
c.368-3C>T Single submitter
c.519-9_519-5del Single submitter
p.Ala1096Val Single submitter ⚠
p.Ala1140= Single submitter intellectual disability, autosomal recessive 43
p.Ala1140Val Single submitter ⚠
p.Ala354Asp Single submitter ⚠
p.Ala485Val Single submitter ⚠
p.Ala498Thr Single submitter ⚠
p.Ala543Thr Single submitter ⚠
p.Ala611Val Single submitter ⚠
p.Ala727Val Single submitter ⚠
p.Ala744Ser Single submitter ⚠
p.Ala95Gly Single submitter ⚠
p.Arg1003Ter Single submitter
p.Arg1065Trp Single submitter ⚠
p.Arg1112Gln Single submitter ⚠
p.Arg139Lys Single submitter ⚠
p.Arg522Lys Single submitter ⚠
p.Arg533Cys Single submitter ⚠
p.Arg685Gln Single submitter ⚠
p.Arg717Gln Single submitter ⚠
p.Arg717Trp Single submitter
p.Arg721Ser Single submitter ⚠
p.Arg761His Single submitter ⚠
p.Arg821Trp Single submitter
p.Arg828Gln Single submitter ⚠
p.Arg871Gln Single submitter ⚠
p.Asn1023Ser Single submitter ⚠
p.Asn1158Ser Single submitter ⚠
p.Asn160= Single submitter
p.Asn273Ser Single submitter ⚠
p.Asn548Ser Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Asn799Ser Single submitter ⚠
p.Asn939Ser Single submitter ⚠
p.Asn952His Single submitter ⚠
p.Asp1068Asn Single submitter ⚠
p.Asp125Glu Single submitter ⚠
p.Asp257Asn Single submitter ⚠
p.Asp499Glu Single submitter ⚠
p.Asp639Asn Single submitter ⚠
p.Asp683Glu Single submitter ⚠
p.Asp696Tyr Single submitter
p.Cys677Tyr Single submitter ⚠
p.Gln1074Ter Single submitter
p.Gln1110Arg Single submitter ⚠
p.Gln396Pro Single submitter ⚠
p.Gln581Arg Single submitter ⚠
p.Gln581Glu Single submitter ⚠
p.Glu1083Ala Single submitter ⚠
p.Glu1083Val Single submitter ⚠
p.Glu239Asp Single submitter ⚠
p.Glu37Gln Single submitter ⚠
p.Glu487Lys Single submitter ⚠
p.Glu544Gly Single submitter
p.Glu595Lys Single submitter ⚠
p.Glu768Gly Single submitter ⚠
p.Glu784Gly Single submitter ⚠
p.Gly1049Ser Single submitter ⚠
p.Gly258Arg Single submitter ⚠
p.Gly320Val Single submitter
p.His1071Tyr Single submitter ⚠
p.His609Asp Single submitter ⚠
p.His631Arg Single submitter ⚠
p.His689Arg Single submitter ⚠
p.His731Arg Single submitter
p.His746Tyr Single submitter ⚠
p.His980Asp Single submitter ⚠
p.Ile1015Val Single submitter ⚠
p.Ile1029Ser Single submitter ⚠
p.Ile295Val Single submitter ⚠
p.Ile328Thr Single submitter ⚠
p.Ile332Thr Single submitter ⚠
p.Ile450Val Single submitter ⚠
p.Ile453Thr Single submitter ⚠
p.Ile516Val Single submitter ⚠
p.Ile53Thr Single submitter ⚠
p.Ile558Thr Single submitter ⚠
p.Ile791Val Single submitter ⚠
p.Ile870Val Single submitter ⚠
p.Leu1103Ser Single submitter ⚠
p.Leu324Ser Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Leu341Met Single submitter ⚠
p.Leu352Val Single submitter ⚠
p.Leu420Phe Single submitter ⚠
p.Leu476Ser Single submitter ⚠
p.Leu650Ser Single submitter ⚠
p.Leu797Phe Single submitter ⚠
p.Leu994Val Single submitter ⚠
p.Lys1138fs Single submitter
p.Lys1173Glu Single submitter ⚠
p.Lys225Arg Single submitter ⚠
p.Lys250Arg Single submitter ⚠
p.Lys335Thr Single submitter ⚠
p.Met1106Val Single submitter ⚠
p.Met189Val Single submitter ⚠
p.Met219Thr Single submitter ⚠
p.Met458Val Single submitter ⚠
p.Met468Val Single submitter ⚠
p.Met489Ile Single submitter ⚠
p.Met489Thr Single submitter ⚠
p.Met645Leu Single submitter ⚠
p.Met923Val Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Phe186Leu Single submitter ⚠
p.Phe261Tyr Single submitter ⚠
p.Phe336Leu Single submitter ⚠
p.Phe711fs Single submitter
p.Pro243Ala Single submitter ⚠
p.Pro360Leu Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Ser1030Gly Single submitter ⚠
p.Ser148Cys Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Ser277Cys Single submitter ⚠
p.Ser379Arg Single submitter ⚠
p.Ser451Arg Single submitter ⚠
p.Ser564Ile Single submitter ⚠
p.Thr1046Ile Single submitter ⚠
p.Thr1139Ala Single submitter ⚠
p.Thr1139Ile Single submitter ⚠
p.Thr1156Arg Single submitter ⚠
p.Thr283Ala Single submitter ⚠
p.Thr351Ile Single submitter ⚠
p.Thr389Ala Single submitter ⚠
p.Thr389Ser Single submitter ⚠
p.Thr456Ile Single submitter ⚠
p.Thr469Ile Single submitter ⚠
p.Thr690Ser Single submitter ⚠
p.Thr736Ile Single submitter ⚠
p.Thr82Ser Single submitter intellectual disability, autosomal recessive 43 ⚠
p.Thr832Met Single submitter ⚠
p.Tyr119Cys Single submitter ⚠
p.Tyr461His Single submitter ⚠
p.Tyr621Cys Single submitter ⚠
p.Tyr798Cys Single submitter ⚠
p.Tyr908His Single submitter ⚠
p.Tyr925Asp Single submitter ⚠
p.Val1025Ile Single submitter ⚠
p.Val162Ile Single submitter ⚠
p.Val278Ala Single submitter ⚠
p.Val299Ala Single submitter ⚠
p.Val299Ile Single submitter ⚠
p.Val407Ile Single submitter ⚠
p.Val496Asp Single submitter ⚠
p.Val501Ala Single submitter ⚠
p.Val501Phe Single submitter ⚠
p.Val536Met Single submitter ⚠
p.Val620_Tyr621insTer Single submitter
p.Val641Ala Single submitter ⚠
p.Val901del Single submitter
p.Val997Ile Single submitter ⚠
p.Ala624Val No assertion criteria WASHC4-related disorder ⚠
p.Pro579fs No assertion criteria intellectual disability, autosomal recessive 43