ATG9A — 93 ClinVar variants

All ClinVar germline ATG9A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 90 flagged for review →

2 Benign · 1 Likely benign · 90 Uncertain significance

Full ATG9A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 90

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 55

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 ATG9A variants

Benign 2

c.1266-5A>G Multiple submitters
p.His161= Multiple submitters

Likely benign 1

p.Ala663Val Single submitter

Uncertain significance 90

p.Ala115Thr Single submitter ⚠
p.Ala2Thr Single submitter ⚠
p.Ala30Thr Single submitter ⚠
p.Ala326Thr Single submitter ⚠
p.Ala389Pro Single submitter ⚠
p.Ala443Thr Single submitter ⚠
p.Ala589Val Single submitter ⚠
p.Ala594Asp Single submitter ⚠
p.Ala622Thr Single submitter ⚠
p.Ala649Thr Single submitter ⚠
p.Ala750Pro Single submitter ⚠
p.Arg10Ser Single submitter ⚠
p.Arg146Gln Single submitter ⚠
p.Arg211His Single submitter ⚠
p.Arg214His Single submitter ⚠
p.Arg231Cys Single submitter ⚠
p.Arg231His Single submitter ⚠
p.Arg233Cys Single submitter ⚠
p.Arg233His Single submitter ⚠
p.Arg245His Single submitter ⚠
p.Arg337Cys Single submitter ⚠
p.Arg356His Single submitter ⚠
p.Arg439His Single submitter ⚠
p.Arg527Cys Single submitter ⚠
p.Arg571Cys Single submitter ⚠
p.Arg586Gln Single submitter ⚠
p.Arg637Gly Single submitter ⚠
p.Arg653His Single submitter ⚠
p.Arg732Cys Single submitter ⚠
p.Arg768Gln Single submitter ⚠
p.Arg784Cys Single submitter ⚠
p.Arg803Gln Single submitter ⚠
p.Asn153Lys Single submitter ⚠
p.Asp427Asn Single submitter ⚠
p.Glu202Asp Single submitter ⚠
p.Glu464Lys Single submitter ⚠
p.Glu601Ala Single submitter ⚠
p.Glu745Lys Single submitter ⚠
p.Gly130Ala Single submitter ⚠
p.Gly236Ser Single submitter ⚠
p.Gly596Arg Single submitter ⚠
p.Gly666Ser Single submitter ⚠
p.Gly676Arg Single submitter ⚠
p.Gly685Arg Single submitter ⚠
p.Gly747Glu Single submitter ⚠
p.His145Leu Single submitter ⚠
p.His348Gln Single submitter ⚠
p.His731Pro Single submitter ⚠
p.His800Tyr Single submitter ⚠
p.Ile126Val Single submitter ⚠
p.Ile392Leu Single submitter ⚠
p.Ile425Met Single submitter ⚠
p.Ile502Thr Single submitter ⚠
p.Ile562Val Single submitter ⚠
p.Leu168Pro Single submitter ⚠
p.Leu206Gln Single submitter ⚠
p.Leu468Arg Single submitter ⚠
p.Leu468Phe Single submitter ⚠
p.Leu557Val Single submitter ⚠
p.Leu599Phe Single submitter ⚠
p.Leu698Gln Single submitter ⚠
p.Phe432Val Single submitter ⚠
p.Pro449Arg Single submitter ⚠
p.Pro532Ala Single submitter ⚠
p.Pro600Ser Single submitter ⚠
p.Pro769Ser Single submitter ⚠
p.Pro833Arg Single submitter ⚠
p.Ser123Gly Single submitter ⚠
p.Ser14Phe Single submitter ⚠
p.Ser33Asn Single submitter ⚠
p.Ser459Leu Single submitter ⚠
p.Ser656Cys Single submitter ⚠
p.Ser741Gly Single submitter ⚠
p.Ser828Leu Single submitter ⚠
p.Ser85Thr Single submitter ⚠
p.Thr105Pro Single submitter ⚠
p.Thr134Ile Single submitter ⚠
p.Thr179Met Single submitter ⚠
p.Thr540Ala Single submitter ⚠
p.Thr606Met Single submitter ⚠
p.Thr81Asn Single submitter ⚠
p.Tyr701Cys Single submitter ⚠
p.Tyr712Cys Single submitter ⚠
p.Tyr89Asn Single submitter ⚠
p.Val141Ile Single submitter ⚠
p.Val29Ile Single submitter ⚠
p.Val513Ile Single submitter ⚠
p.Val526Ile Single submitter ⚠
p.Val794Gly Single submitter ⚠
p.Val87Met Single submitter ⚠