CALHM1 — 72 ClinVar variants

All ClinVar germline CALHM1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 72 flagged for review →

1 Likely pathogenic · 1 Benign · 70 Uncertain significance

Full CALHM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 72

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.

CALHM1 p.Arg154His Likely pathogenic Single submitter

Predictors lean, ClinVar uncertain 37

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

Predictors split 34

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

All CALHM1 variants

Likely pathogenic 1

p.Arg154His Single submitter ⚠

Benign 1

p.Ala153Thr Multiple submitters ⚠

Uncertain significance 70

p.Ala107Thr Single submitter ⚠
p.Ala110Val Single submitter ⚠
p.Ala137Thr Single submitter ⚠
p.Ala172Pro Single submitter ⚠
p.Ala186Val Single submitter ⚠
p.Ala212Ser Single submitter ⚠
p.Ala213Val Single submitter ⚠
p.Ala272Thr Single submitter ⚠
p.Ala283Val Single submitter ⚠
p.Ala328Ser Single submitter ⚠
p.Ala50Val Single submitter ⚠
p.Ala54Glu Single submitter ⚠
p.Ala54Thr Single submitter ⚠
p.Ala59Thr Single submitter ⚠
p.Arg158Trp Single submitter ⚠
p.Arg173Gln Single submitter ⚠
p.Arg173Gly Single submitter ⚠
p.Arg181His Single submitter ⚠
p.Arg203Cys Single submitter ⚠
p.Arg203His Single submitter ⚠
p.Arg206Gln Single submitter ⚠
p.Arg228His Single submitter ⚠
p.Arg228Ser Single submitter ⚠
p.Arg291Cys Single submitter ⚠
p.Arg291His Single submitter ⚠
p.Arg333Gln Single submitter ⚠
p.Arg336Cys Single submitter ⚠
p.Arg6Gln Single submitter ⚠
p.Arg89Gln Single submitter ⚠
p.Arg89Trp Single submitter ⚠
p.Arg97His Single submitter ⚠
p.Asn325Lys Single submitter ⚠
p.Asp168Asn Single submitter ⚠
p.Asp232Asn Single submitter ⚠
p.Cys42Arg Single submitter ⚠
p.Glu151Lys Single submitter ⚠
p.Glu319Lys Single submitter ⚠
p.Glu338Lys Single submitter ⚠
p.Gly139Ala Single submitter ⚠
p.Gly141Ser Single submitter ⚠
p.Gly25Ser Single submitter ⚠
p.Gly265Glu Single submitter ⚠
p.Gly297Cys Single submitter ⚠
p.Gly326Ser Single submitter ⚠
p.Ile247Val Single submitter ⚠
p.Ile8Asn Single submitter ⚠
p.Leu108Phe Single submitter ⚠
p.Leu69Arg Single submitter ⚠
p.Met103Lys Single submitter ⚠
p.Met254Thr Single submitter ⚠
p.Met34Leu Single submitter ⚠
p.Met71Ile Single submitter ⚠
p.Met77Leu Single submitter ⚠
p.Met7Ile Single submitter ⚠
p.Phe242Tyr Single submitter ⚠
p.Pro111Ser Single submitter ⚠
p.Pro162Leu Single submitter ⚠
p.Pro311Leu Single submitter ⚠
p.Pro321Thr Single submitter ⚠
p.Pro93Ser Single submitter ⚠
p.Ser102Phe Single submitter ⚠
p.Ser53Gly Single submitter ⚠
p.Thr118Lys Single submitter ⚠
p.Thr118Met Single submitter ⚠
p.Thr234Met Single submitter ⚠
p.Thr278Met Single submitter ⚠
p.Val135Met Single submitter ⚠
p.Val159Met Single submitter ⚠
p.Val192Leu Single submitter ⚠
p.Val201Met Single submitter ⚠