CHAF1A — 153 ClinVar variants

All ClinVar germline CHAF1A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 132 flagged for review →

1 Pathogenic · 6 Likely pathogenic · 1 Benign · 11 Likely benign · 134 Uncertain significance

Full CHAF1A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 132

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 97

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

Predictors split 35

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

All CHAF1A variants

Pathogenic 1

p.Trp668Ter Single submitter

Likely pathogenic 6

c.1377+1G>A No assertion criteria craniofacial microsomia
c.1604+1G>A No assertion criteria craniofacial microsomia
p.Cys563_Glu564delinsTer No assertion criteria craniofacial microsomia
p.Thr211fs No assertion criteria craniofacial microsomia
p.Thr293fs No assertion criteria craniofacial microsomia
p.Trp690Ter No assertion criteria craniofacial microsomia

Benign 1

p.Ala70= Multiple submitters

Likely benign 11

c.2771-9G>A Single submitter
p.Ala708Thr Single submitter
p.Ala70Thr Single submitter
p.Arg730Lys Single submitter
p.Gln57Arg Single submitter
p.Glu107Lys Single submitter
p.Glu733Gln Single submitter
p.Gly944Ser Single submitter
p.Ile792Val Single submitter
p.Met265Val Single submitter
p.Thr943Ala Single submitter

Uncertain significance 134

p.Ala140Gly Single submitter ⚠
p.Ala16Pro Single submitter ⚠
p.Ala193Ser Single submitter ⚠
p.Ala193Thr Single submitter ⚠
p.Ala247Pro Single submitter ⚠
p.Ala486Thr Single submitter ⚠
p.Ala583Thr Single submitter ⚠
p.Ala588Ser Single submitter ⚠
p.Ala697Ser Single submitter ⚠
p.Ala697Thr Single submitter ⚠
p.Ala70Val Single submitter ⚠
p.Ala922Thr Single submitter ⚠
p.Ala931Ser Single submitter ⚠
p.Arg13Lys Single submitter ⚠
p.Arg151Gln Single submitter ⚠
p.Arg205Trp Single submitter ⚠
p.Arg319His Single submitter ⚠
p.Arg320Ile Single submitter ⚠
p.Arg351His Single submitter ⚠
p.Arg387Gln Single submitter ⚠
p.Arg387Trp Single submitter ⚠
p.Arg407Trp Single submitter ⚠
p.Arg483His Single submitter ⚠
p.Arg484Gln Single submitter ⚠
p.Arg528Gln Single submitter ⚠
p.Arg528Trp Single submitter ⚠
p.Arg542His Single submitter ⚠
p.Arg677Gly Single submitter ⚠
p.Arg677His Single submitter ⚠
p.Arg728Gln Single submitter ⚠
p.Arg763Trp Single submitter ⚠
p.Arg774Gln Single submitter ⚠
p.Arg774Trp Single submitter ⚠
p.Arg797Trp Single submitter ⚠
p.Arg886His Single submitter ⚠
p.Arg887Trp Single submitter ⚠
p.Asp128Ala Single submitter ⚠
p.Asp496Asn Single submitter ⚠
p.Asp51Asn Single submitter ⚠
p.Asp546Glu Single submitter ⚠
p.Asp546Gly Single submitter ⚠
p.Asp56Asn Single submitter ⚠
p.Asp585Glu Single submitter ⚠
p.Asp627Val Single submitter ⚠
p.Asp653Asn Single submitter ⚠
p.Asp695Gly Single submitter ⚠
p.Asp699Asn Single submitter ⚠
p.Asp732Glu Single submitter ⚠
p.Cys181Gly Single submitter ⚠
p.Cys710Arg Single submitter ⚠
p.Cys761Tyr Single submitter ⚠
p.Gln222Glu Single submitter ⚠
p.Glu270Lys Single submitter ⚠
p.Glu277Lys Single submitter ⚠
p.Glu358Lys Single submitter ⚠
p.Glu369Gln Single submitter ⚠
p.Glu426Asp Single submitter ⚠
p.Glu550Lys Single submitter ⚠
p.Glu550Val Single submitter ⚠
p.Glu733Lys Single submitter ⚠
p.Glu76Gly Single submitter ⚠
p.Glu788Lys Single submitter ⚠
p.Glu809Lys Single submitter ⚠
p.Gly11Ser Single submitter ⚠
p.Gly155Ala Single submitter ⚠
p.Gly345Asp Single submitter ⚠
p.Gly504= Single submitter
p.Gly521Glu Single submitter ⚠
p.Gly545Asp Single submitter ⚠
p.Gly618Arg Single submitter ⚠
p.Gly625Arg Single submitter ⚠
p.Gly687Arg Single submitter ⚠
p.Gly771Ser Single submitter ⚠
p.Gly82Cys Single submitter ⚠
p.Gly82Val Single submitter ⚠
p.Gly875Val Single submitter ⚠
p.Gly934Arg Single submitter ⚠
p.Gly936Ala Single submitter ⚠
p.Gly937Arg Single submitter ⚠
p.Gly937Val Single submitter ⚠
p.His821Arg Single submitter ⚠
p.Ile110Thr Single submitter ⚠
p.Ile916Met Single submitter ⚠
p.Leu130Phe Single submitter ⚠
p.Leu210Pro Single submitter ⚠
p.Leu766Phe Single submitter ⚠
p.Leu781Arg Single submitter ⚠
p.Lys234Glu Single submitter ⚠
p.Lys374Gln Single submitter ⚠
p.Lys884Thr Single submitter ⚠
p.Lys95Met Single submitter ⚠
p.Met53Val Single submitter ⚠
p.Met897Val Single submitter ⚠
p.Phe325Ile Single submitter ⚠
p.Phe487Leu Single submitter ⚠
p.Pro208Leu Single submitter ⚠
p.Pro250Leu Single submitter ⚠
p.Pro251Arg Single submitter ⚠
p.Pro267Arg Single submitter ⚠
p.Pro299Leu Single submitter ⚠
p.Pro302Arg Single submitter ⚠
p.Pro313Leu Single submitter ⚠
p.Pro586Arg Single submitter ⚠
p.Pro716Leu Single submitter ⚠
p.Pro773Ala Single submitter ⚠
p.Pro776Ser Single submitter ⚠
p.Pro786His Single submitter ⚠
p.Pro836Leu Single submitter ⚠
p.Pro846Ser Single submitter ⚠
p.Pro857Ser Single submitter ⚠
p.Pro920Leu Single submitter ⚠
p.Pro952Leu Single submitter ⚠
p.Ser123Leu Single submitter ⚠
p.Ser269Gly Single submitter ⚠
p.Ser286Ala Single submitter ⚠
p.Ser315Tyr Single submitter ⚠
p.Ser503Arg Single submitter ⚠
p.Ser65Arg Single submitter ⚠
p.Ser726Phe Single submitter ⚠
p.Ser844Leu Single submitter ⚠
p.Thr154Ser Single submitter ⚠
p.Thr175Ala Single submitter ⚠
p.Thr454Ile Single submitter ⚠
p.Thr783Ile Single submitter ⚠
p.Thr859Met Single submitter ⚠
p.Thr904Ala Single submitter ⚠
p.Thr904Met Single submitter ⚠
p.Val241Gly Single submitter ⚠
p.Val271Met Single submitter ⚠
p.Val326Ile Single submitter ⚠
p.Val478Ile Single submitter ⚠
p.Val538Ile Single submitter ⚠
p.Val689Met Single submitter ⚠
c.1948-1G>A No assertion criteria craniofacial microsomia 1