SEC31A — 150 ClinVar variants
All ClinVar germline SEC31A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 104 flagged for review →
1 Pathogenic · 11 Benign · 24 Likely benign · 114 Uncertain significance
Full SEC31A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 104
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 92
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SEC31A p.Asp84Gly Uncertain significance Multiple submitters
-
SEC31A p.Cys458Trp
Uncertain significance
Multiple submitters
neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- SEC31A p.Pro945Ser Uncertain significance Multiple submitters
- SEC31A p.Ala1042Val Uncertain significance Single submitter
- SEC31A p.Ala116Ser Uncertain significance Single submitter
- SEC31A p.Ala602Thr Uncertain significance Single submitter
- SEC31A p.Ala985Val Uncertain significance Single submitter
- SEC31A p.Arg1175Gly Uncertain significance Single submitter
- SEC31A p.Arg594Ser Uncertain significance Single submitter
- SEC31A p.Arg612Gln Uncertain significance Single submitter
- SEC31A p.Arg728Gln Uncertain significance Single submitter
- SEC31A p.Arg783His Uncertain significance Single submitter
- SEC31A p.Asn1216Ser Uncertain significance Single submitter
- SEC31A p.Asn778Ser Uncertain significance Single submitter
- SEC31A p.Asn778Tyr Uncertain significance Single submitter
-
SEC31A p.Asp1114Glu
Uncertain significance
Single submitter
neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- SEC31A p.Asp719Tyr Uncertain significance Single submitter
- SEC31A p.Asp7Gly Uncertain significance Single submitter
- SEC31A p.Asp80Tyr Uncertain significance Single submitter
- SEC31A p.Cys1130Trp Uncertain significance Single submitter
- SEC31A p.Gln345Glu Uncertain significance Single submitter
- SEC31A p.Gln420Pro Uncertain significance Single submitter
- SEC31A p.Gln446His Uncertain significance Single submitter
- SEC31A p.Gln450Arg Uncertain significance Single submitter
- SEC31A p.Gln709Arg Uncertain significance Single submitter
- SEC31A p.Glu1012Val Uncertain significance Single submitter
- SEC31A p.Glu1085Asp Uncertain significance Single submitter
- SEC31A p.Glu202Asp Uncertain significance Single submitter
- SEC31A p.Glu531Ala Uncertain significance Single submitter
- SEC31A p.Glu537Gln Uncertain significance Single submitter
- SEC31A p.Glu547Lys Uncertain significance Single submitter
- SEC31A p.Glu550Lys Uncertain significance Single submitter
- SEC31A p.Glu792Gly Uncertain significance Single submitter
- SEC31A p.Glu798Lys Uncertain significance Single submitter
- SEC31A p.Glu805Lys Uncertain significance Single submitter
- SEC31A p.Gly886Arg Uncertain significance Single submitter
- SEC31A p.His215Arg Uncertain significance Single submitter
- SEC31A p.His425Arg Uncertain significance Single submitter
- SEC31A p.His797Tyr Uncertain significance Single submitter
- SEC31A p.Ile171Val Uncertain significance Single submitter
- SEC31A p.Ile333Val Uncertain significance Single submitter
- SEC31A p.Ile379Thr Uncertain significance Single submitter
- SEC31A p.Ile379Val Uncertain significance Single submitter
- SEC31A p.Ile429Val Uncertain significance Single submitter
- SEC31A p.Ile462Thr Uncertain significance Single submitter
- SEC31A p.Ile98Val Uncertain significance Single submitter
- SEC31A p.Leu275Met Uncertain significance Single submitter
- SEC31A p.Leu319Phe Uncertain significance Single submitter
- SEC31A p.Leu48Ser Uncertain significance Single submitter
- SEC31A p.Leu610Phe Uncertain significance Single submitter
- SEC31A p.Leu671Ile Uncertain significance Single submitter
- SEC31A p.Leu701Ser Uncertain significance Single submitter
- SEC31A p.Lys1009Glu Uncertain significance Single submitter
- SEC31A p.Lys1110Thr Uncertain significance Single submitter
- SEC31A p.Lys615Arg Uncertain significance Single submitter
- SEC31A p.Lys811Arg Uncertain significance Single submitter
- SEC31A p.Met1010Val Uncertain significance Single submitter
- SEC31A p.Met823Lys Uncertain significance Single submitter
- SEC31A p.Met845Val Uncertain significance Single submitter
- SEC31A p.Phe885Leu Uncertain significance Single submitter
- SEC31A p.Phe885Val Uncertain significance Single submitter
- SEC31A p.Pro1031Arg Uncertain significance Single submitter
- SEC31A p.Pro1043Leu Uncertain significance Single submitter
- SEC31A p.Pro1103Leu Uncertain significance Single submitter
- SEC31A p.Pro168Ser Uncertain significance Single submitter
- SEC31A p.Pro662Leu Uncertain significance Single submitter
- SEC31A p.Pro810Ser Uncertain significance Single submitter
- SEC31A p.Pro824Ser Uncertain significance Single submitter
- SEC31A p.Pro838Arg Uncertain significance Single submitter
- SEC31A p.Pro840Ser Uncertain significance Single submitter
- SEC31A p.Pro869Leu Uncertain significance Single submitter
- SEC31A p.Pro944Ser Uncertain significance Single submitter
- SEC31A p.Pro970Arg Uncertain significance Single submitter
- SEC31A p.Pro971Thr Uncertain significance Single submitter
- SEC31A p.Ser1168Gly Uncertain significance Single submitter
- SEC31A p.Ser337Asn Uncertain significance Single submitter
- SEC31A p.Ser397Ala Uncertain significance Single submitter
- SEC31A p.Ser475Ala Uncertain significance Single submitter
- SEC31A p.Ser682Asn Uncertain significance Single submitter
- SEC31A p.Thr1104Ile Uncertain significance Single submitter
- SEC31A p.Thr194Ile Uncertain significance Single submitter
- SEC31A p.Thr626Ser Uncertain significance Single submitter
- SEC31A p.Thr734Ile Uncertain significance Single submitter
- SEC31A p.Thr739Ser Uncertain significance Single submitter
- SEC31A p.Thr973Ala Uncertain significance Single submitter
- SEC31A p.Tyr617Cys Uncertain significance Single submitter
- SEC31A p.Tyr617His Uncertain significance Single submitter
- SEC31A p.Tyr692Cys Uncertain significance Single submitter
- SEC31A p.Val1004Ile Uncertain significance Single submitter
- SEC31A p.Val130Leu Uncertain significance Single submitter
- SEC31A p.Val698Leu Uncertain significance Single submitter
- SEC31A p.Val742Ile Uncertain significance Single submitter
Predictors split 12
The independent predictors disagree with each other — read with care.
- SEC31A p.Arg441Gln Uncertain significance Single submitter
- SEC31A p.Asn201Lys Uncertain significance Single submitter
- SEC31A p.Asn581Ser Uncertain significance Single submitter
- SEC31A p.Asp236Asn Uncertain significance Single submitter
- SEC31A p.Asp236Glu Uncertain significance Single submitter
- SEC31A p.Ile600Met Uncertain significance Single submitter
- SEC31A p.Phe665Leu Uncertain significance Single submitter
- SEC31A p.Ser1163Pro Uncertain significance Single submitter
- SEC31A p.Ser38Gly Uncertain significance Single submitter
- SEC31A p.Ser666Leu Uncertain significance Single submitter
- SEC31A p.Tyr893Cys Uncertain significance Single submitter
- SEC31A p.Val195Leu Uncertain significance Single submitter
All SEC31A variants
Pathogenic 1
- p.Ala927fs No assertion criteria neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
Benign 11
- c.1045-26G>T Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- c.2154+36G>C Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- c.2503-29C>A Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- c.640-4T>G Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- p.Arg199= Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- p.Gly336= Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies
- p.Pro1031Leu Multiple submitters
- p.Pro841Leu Multiple submitters
- p.Tyr659= Multiple submitters
- c.782+542G>T Single submitter
- p.Ile263Val Single submitter
Likely benign 24
- c.2154+8C>T Multiple submitters
- c.1703-19T>C Single submitter
- c.1882-11C>T Single submitter
- c.3291+5C>T Single submitter
- c.402+3T>G Single submitter
- c.79+20G>T Single submitter
- p.Ala985= Single submitter
- p.Asn456Lys Single submitter
- p.Asn755= Single submitter
- p.Gly680= Single submitter
- p.Gly956= Single submitter
- p.His543= Single submitter
- p.Pro1082= Single submitter
- p.Pro167= Single submitter
- p.Pro662= Single submitter
- p.Pro958= Single submitter
- p.Ser233= Single submitter
- p.Thr194= Single submitter
- p.Thr39= Single submitter
- p.Thr630= Single submitter
- p.Tyr926= Single submitter
- p.Val1066Ile Single submitter
- c.2968+1G>T No assertion criteria SEC31A-related disorder
- p.Thr303Lys No assertion criteria SEC31A-related disorder
Uncertain significance 114
- p.Arg486His Multiple submitters
- p.Asp84Gly Multiple submitters ⚠
- p.Cys458Trp Multiple submitters neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies ⚠
- p.Pro945Ser Multiple submitters ⚠
- p.Ala1042Val Single submitter ⚠
- p.Ala116Ser Single submitter ⚠
- p.Ala602Thr Single submitter ⚠
- p.Ala985Val Single submitter ⚠
- p.Arg1175Gly Single submitter ⚠
- p.Arg441Gln Single submitter ⚠
- p.Arg594Ser Single submitter ⚠
- p.Arg612Gln Single submitter ⚠
- p.Arg728Gln Single submitter ⚠
- p.Arg783Cys Single submitter
- p.Arg783His Single submitter ⚠
- p.Asn1216Ser Single submitter ⚠
- p.Asn153Ile Single submitter
- p.Asn201Lys Single submitter ⚠
- p.Asn315fs Single submitter
- p.Asn581Ser Single submitter ⚠
- p.Asn778Ser Single submitter ⚠
- p.Asn778Tyr Single submitter ⚠
- p.Asp1114Glu Single submitter neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies ⚠
- p.Asp236Asn Single submitter ⚠
- p.Asp236Glu Single submitter ⚠
- p.Asp325Asn Single submitter
- p.Asp719Tyr Single submitter ⚠
- p.Asp7Gly Single submitter ⚠
- p.Asp80Tyr Single submitter ⚠
- p.Cys1130Trp Single submitter ⚠
- p.Gln345Glu Single submitter ⚠
- p.Gln420Pro Single submitter ⚠
- p.Gln446His Single submitter ⚠
- p.Gln450Arg Single submitter ⚠
- p.Gln709Arg Single submitter ⚠
- p.Glu1012Val Single submitter ⚠
- p.Glu1085Asp Single submitter ⚠
- p.Glu202Asp Single submitter ⚠
- p.Glu531Ala Single submitter ⚠
- p.Glu537Gln Single submitter ⚠
- p.Glu547Lys Single submitter ⚠
- p.Glu550Lys Single submitter ⚠
- p.Glu792Gly Single submitter ⚠
- p.Glu798Lys Single submitter ⚠
- p.Glu805Lys Single submitter ⚠
- p.Gly886Arg Single submitter ⚠
- p.His215Arg Single submitter ⚠
- p.His425Arg Single submitter ⚠
- p.His797Tyr Single submitter ⚠
- p.Ile171Val Single submitter ⚠
- p.Ile333Val Single submitter ⚠
- p.Ile379Thr Single submitter ⚠
- p.Ile379Val Single submitter ⚠
- p.Ile429Val Single submitter ⚠
- p.Ile462Thr Single submitter ⚠
- p.Ile600Met Single submitter ⚠
- p.Ile90Thr Single submitter
- p.Ile98Val Single submitter ⚠
- p.Leu1126Val Single submitter
- p.Leu275Met Single submitter ⚠
- p.Leu319Phe Single submitter ⚠
- p.Leu48Ser Single submitter ⚠
- p.Leu610Phe Single submitter ⚠
- p.Leu671Ile Single submitter ⚠
- p.Leu701Ser Single submitter ⚠
- p.Lys1009Glu Single submitter ⚠
- p.Lys1110Thr Single submitter ⚠
- p.Lys615Arg Single submitter ⚠
- p.Lys811Arg Single submitter ⚠
- p.Met1010Val Single submitter ⚠
- p.Met823Lys Single submitter ⚠
- p.Met845Val Single submitter ⚠
- p.Phe665Leu Single submitter ⚠
- p.Phe885Leu Single submitter ⚠
- p.Phe885Val Single submitter ⚠
- p.Pro1031Arg Single submitter ⚠
- p.Pro1043Leu Single submitter ⚠
- p.Pro1103Leu Single submitter ⚠
- p.Pro168Ser Single submitter ⚠
- p.Pro386Leu Single submitter
- p.Pro662Leu Single submitter ⚠
- p.Pro714Leu Single submitter
- p.Pro810Ser Single submitter ⚠
- p.Pro824Ser Single submitter ⚠
- p.Pro838Arg Single submitter ⚠
- p.Pro840Ser Single submitter ⚠
- p.Pro869Leu Single submitter ⚠
- p.Pro944Ser Single submitter ⚠
- p.Pro970Arg Single submitter ⚠
- p.Pro971Thr Single submitter ⚠
- p.Ser1163Pro Single submitter ⚠
- p.Ser1168Gly Single submitter ⚠
- p.Ser337Asn Single submitter ⚠
- p.Ser38Gly Single submitter ⚠
- p.Ser397Ala Single submitter ⚠
- p.Ser475Ala Single submitter ⚠
- p.Ser666Leu Single submitter ⚠
- p.Ser682Asn Single submitter ⚠
- p.Thr1104Ile Single submitter ⚠
- p.Thr194Ile Single submitter ⚠
- p.Thr361Ile Single submitter
- p.Thr626Ser Single submitter ⚠
- p.Thr734Ile Single submitter ⚠
- p.Thr739Ser Single submitter ⚠
- p.Thr973Ala Single submitter ⚠
- p.Tyr617Cys Single submitter ⚠
- p.Tyr617His Single submitter ⚠
- p.Tyr692Cys Single submitter ⚠
- p.Tyr893Cys Single submitter ⚠
- p.Val1004Ile Single submitter ⚠
- p.Val130Leu Single submitter ⚠
- p.Val195Leu Single submitter ⚠
- p.Val698Leu Single submitter ⚠
- p.Val742Ile Single submitter ⚠