SMARCA1 — 182 ClinVar variants

All ClinVar germline SMARCA1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 99 flagged for review →

5 Pathogenic · 13 Likely pathogenic · 3 Conflicting · 4 Benign · 15 Likely benign · 142 Uncertain significance

Full SMARCA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 99

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 79

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

Predictors split 20

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

All SMARCA1 variants

Pathogenic 5

p.Arg448Ter Single submitter
p.Arg751Ter Single submitter
p.Arg928Ter Single submitter
p.Arg993Ter Single submitter
p.Trp1002Ter Single submitter

Likely pathogenic 13

p.Arg229Ter Single submitter neurodevelopmental disorder
p.Arg253Ter Single submitter neurodevelopmental disorder
p.Arg607Ter Single submitter SMARCA1-related disorder
p.Arg91Ter Single submitter neurodevelopmental disorder
p.Asn658Ter Single submitter neurodevelopmental disorder
p.Gln3Ter Single submitter Abnormal brain morphology
p.Gln65Ter Single submitter non-syndromic X-linked intellectual disability
p.Gln708Ter Single submitter neurodevelopmental disorder
p.Glu412Lys Single submitter
p.Leu138Ter Single submitter non-syndromic X-linked intellectual disability
p.Leu357Ter Single submitter neurodevelopmental disorder
p.Leu358fs Single submitter neurodevelopmental disorder
p.Pro182fs Single submitter neurodevelopmental disorder

Conflicting classifications of pathogenicity 3

p.Arg189Ter Single submitter neurodevelopmental disorder
p.Arg306Ter Single submitter neurodevelopmental disorder
p.Arg706Cys Single submitter ⚠

Benign 4

p.Gly837Ala Multiple submitters
p.Pro775Gln Multiple submitters
p.Arg275Cys Single submitter
p.Thr536= Single submitter

Likely benign 15

c.1504+7A>G Single submitter
c.2566-9T>G Single submitter
p.Ala72Val Single submitter
p.Arg1007= Single submitter
p.Arg448Gln Single submitter
p.Arg795Cys Single submitter
p.Gln3His Single submitter
p.Glu803= Single submitter
p.His388= Single submitter
p.Leu642= Single submitter
p.Leu853= Single submitter
p.Lys443= Single submitter
p.Lys55Asn Single submitter
p.Thr102= Single submitter
p.Val22Leu Single submitter

Uncertain significance 142

p.Ala39Thr Multiple submitters ⚠
p.Ala48Glu Multiple submitters ⚠
p.Ala6Pro Multiple submitters ⚠
p.Arg751Gln Multiple submitters neurodevelopmental disorder ⚠
p.Asp721Asn Multiple submitters neurodevelopmental disorder ⚠
p.Gly30Arg Multiple submitters ⚠
p.Lys680Glu Multiple submitters
p.Met1028Ile Multiple submitters
p.Pro117Ala Multiple submitters ⚠
c.1278-9A>G Single submitter
c.2098-7C>T Single submitter
c.2818-8A>G Single submitter
c.3030+1G>A Single submitter
c.3030+1G>C Single submitter
c.3141+11C>T Single submitter neurodevelopmental disorder ⚠
c.428+3A>T Single submitter
p.Ala19Thr Single submitter ⚠
p.Ala49Thr Single submitter ⚠
p.Ala661Thr Single submitter ⚠
p.Ala70Thr Single submitter ⚠
p.Ala758Thr Single submitter ⚠
p.Ala827Gly Single submitter ⚠
p.Arg1035fs Single submitter neurodevelopmental disorder
p.Arg1035Lys Single submitter ⚠
p.Arg1041Trp Single submitter
p.Arg127Cys Single submitter ⚠
p.Arg189Gln Single submitter neurodevelopmental disorder ⚠
p.Arg253= Single submitter
p.Arg259Gly Single submitter neurodevelopmental disorder ⚠
p.Arg259His Single submitter ⚠
p.Arg259Pro Single submitter ⚠
p.Arg275His Single submitter ⚠
p.Arg335His Single submitter ⚠
p.Arg457Gln Single submitter ⚠
p.Arg525His Single submitter ⚠
p.Arg531Gln Single submitter ⚠
p.Arg610Gly Single submitter ⚠
p.Arg618Cys Single submitter ⚠
p.Arg641Thr Single submitter ⚠
p.Arg768Cys Single submitter ⚠
p.Arg768His Single submitter ⚠
p.Arg808Gln Single submitter ⚠
p.Arg863Ter Single submitter
p.Arg921Cys Single submitter ⚠
p.Arg929Lys Single submitter
p.Arg951His Single submitter ⚠
p.Arg981Lys Single submitter ⚠
p.Asn230Asp Single submitter ⚠
p.Asn246Ser Single submitter ⚠
p.Asn363Ser Single submitter ⚠
p.Asn484Ser Single submitter ⚠
p.Asn564Asp Single submitter ⚠
p.Asn756Ser Single submitter
p.Asn785Ser Single submitter
p.Asn872Ser Single submitter
p.Asp367Glu Single submitter ⚠
p.Asp4Asn Single submitter ⚠
p.Asp4Gly Single submitter ⚠
p.Asp625Gly Single submitter ⚠
p.Asp836Asn Single submitter
p.Asp90Asn Single submitter
p.Asp911Glu Single submitter
p.Cys377Tyr Single submitter ⚠
p.Gln136Arg Single submitter neurodevelopmental disorder ⚠
p.Gln381Arg Single submitter ⚠
p.Gln656Arg Single submitter
p.Gln855Arg Single submitter ⚠
p.Glu1031Gly Single submitter ⚠
p.Glu156Val Single submitter ⚠
p.Glu250Asp Single submitter ⚠
p.Glu250Gly Single submitter ⚠
p.Glu45Lys Single submitter ⚠
p.Glu500Asp Single submitter ⚠
p.Glu681Lys Single submitter
p.Glu705Gly Single submitter
p.Glu732del Single submitter
p.Glu752Lys Single submitter ⚠
p.Glu771Lys Single submitter neurodevelopmental disorder ⚠
p.Glu801Ter Single submitter
p.Glu830Gly Single submitter ⚠
p.Glu894Val Single submitter neurodevelopmental disorder ⚠
p.Gly38Val Single submitter ⚠
p.Gly53Ser Single submitter ⚠
p.Gly580Arg Single submitter SMARCA1-related disorder ⚠
p.Gly741Cys Single submitter
p.His671Gln Single submitter
p.Ile1004Met Single submitter
p.Ile1023fs Single submitter
p.Ile1023Thr Single submitter X-linked intellectual disability ⚠
p.Ile219Ser Single submitter ⚠
p.Ile24Thr Single submitter ⚠
p.Ile310Val Single submitter ⚠
p.Ile435Thr Single submitter ⚠
p.Ile557Val Single submitter ⚠
p.Ile645Val Single submitter
p.Ile647Thr Single submitter neurodevelopmental disorder ⚠
p.Ile835Thr Single submitter ⚠
p.Leu183Pro Single submitter ⚠
p.Leu726Ter Single submitter
p.Leu805Phe Single submitter
p.Leu99Pro Single submitter ⚠
p.Lys400Glu Single submitter ⚠
p.Lys567Arg Single submitter
p.Lys59Gln Single submitter ⚠
p.Lys614Glu Single submitter
p.Lys699Glu Single submitter ⚠
p.Lys71Glu Single submitter ⚠
p.Lys739= Single submitter
p.Lys776Glu Single submitter ⚠
p.Lys834Asn Single submitter ⚠
p.Lys834Glu Single submitter
p.Lys93Asn Single submitter ⚠
p.Met1028Val Single submitter
p.Met432Thr Single submitter neurodevelopmental disorder ⚠
p.Met79Thr Single submitter ⚠
p.Phe1003Leu Single submitter neurodevelopmental disorder ⚠
p.Phe560Leu Single submitter neurodevelopmental disorder
p.Phe797Leu Single submitter
p.Phe998Leu Single submitter ⚠
p.Pro175Ser Single submitter ⚠
p.Pro256Leu Single submitter neurodevelopmental disorder ⚠
p.Pro29His Single submitter ⚠
p.Pro537Leu Single submitter ⚠
p.Pro73Ser Single submitter ⚠
p.Pro824Leu Single submitter neurodevelopmental disorder ⚠
p.Pro840Ser Single submitter
p.Pro843Ala Single submitter ⚠
p.Ser165Cys Single submitter ⚠
p.Ser714Cys Single submitter ⚠
p.Ser931Gly Single submitter
p.Thr1018Ile Single submitter ⚠
p.Thr118Ile Single submitter neurodevelopmental disorder ⚠
p.Thr428Ile Single submitter ⚠
p.Thr477fs Single submitter
p.Thr47Ala Single submitter ⚠
p.Thr47Ser Single submitter ⚠
p.Thr858Ala Single submitter
p.Tyr177His Single submitter ⚠
p.Val12Ala Single submitter ⚠
p.Val293Ala Single submitter SMARCA1-related disorder
p.Val505Ala Single submitter neurodevelopmental disorder ⚠
p.Thr477Ser No assertion criteria