VAMP2 — 52 ClinVar variants
All ClinVar germline VAMP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 15 flagged for review →
8 Pathogenic · 6 Likely pathogenic · 1 Conflicting · 1 Benign · 18 Likely benign · 18 Uncertain significance
Full VAMP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 15
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 6
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
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VAMP2 p.Ala74Val
Uncertain significance
Multiple submitters
neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
- VAMP2 p.Ala67Val Uncertain significance Single submitter
- VAMP2 p.Arg66His Uncertain significance Single submitter
- VAMP2 p.Arg86Cys Uncertain significance Single submitter
- VAMP2 p.Leu63Pro Uncertain significance Single submitter
-
VAMP2 p.Lys94Gln
Uncertain significance
Single submitter
Inborn genetic diseases
Predictors split 9
The independent predictors disagree with each other — read with care.
- VAMP2 p.Ala104Thr Uncertain significance Single submitter
-
VAMP2 p.Arg86His
Uncertain significance
Single submitter
Inborn genetic diseases
- VAMP2 p.Asp40Asn Uncertain significance Single submitter
- VAMP2 p.Asp68Glu Uncertain significance Single submitter
-
VAMP2 p.Ile106Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
VAMP2 p.Ile109Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
VAMP2 p.Ile110Leu
Conflicting
Single submitter
Inborn genetic diseases
- VAMP2 p.Pro9Leu Uncertain significance Single submitter
- VAMP2 p.Val53Ile Uncertain significance Single submitter
All VAMP2 variants
Pathogenic 8
- c.128_130del Single submitter Severe neurodevelopmental delay
- p.Arg56Ter Single submitter
- p.Arg66Pro Single submitter
- p.Met1Val Single submitter
- p.Glu78Ala No assertion criteria neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
- p.Ile45del No assertion criteria neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
- p.Phe77Ser No assertion criteria neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
- p.Ser75Pro No assertion criteria neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
Likely pathogenic 6
- c.2+2T>C Single submitter VAMP2-related disorder
- p.Arg56Leu Single submitter
- p.Gln76Ter Single submitter neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
- p.Gly73Trp Single submitter
- p.Tyr113fs Single submitter
- p.Val50Met Single submitter neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
Conflicting classifications of pathogenicity 1
- p.Ile110Leu Single submitter Inborn genetic diseases ⚠
Benign 1
- c.334+12G>C Multiple submitters neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
Likely benign 18
- c.3-101G>T Multiple submitters
- p.Ile98= Multiple submitters
- p.Leu54= Multiple submitters
- c.124-3C>T Single submitter Inborn genetic diseases
- c.3-58C>G Single submitter
- c.335-15C>A Single submitter
- c.-13C>G Single submitter
- c.-18C>T Single submitter
- c.-4del Single submitter
- c.-6C>T Single submitter
- c.-8C>T Single submitter
- p.Ala72= Single submitter
- p.Asp64= Single submitter
- p.Cys103= Single submitter
- p.Leu60= Single submitter
- p.Leu84= Single submitter
- p.Asn49= No assertion criteria VAMP2-related disorder
- p.Ser61= No assertion criteria VAMP2-related disorder
Uncertain significance 18
- p.Ala74Val Multiple submitters neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements ⚠
- c.124-1G>C Single submitter
- p.Ala104Thr Single submitter ⚠
- p.Ala12_Gly15del Single submitter
- p.Ala67Val Single submitter ⚠
- p.Arg66His Single submitter ⚠
- p.Arg86Cys Single submitter ⚠
- p.Arg86His Single submitter Inborn genetic diseases ⚠
- p.Asp40Asn Single submitter ⚠
- p.Asp68Glu Single submitter ⚠
- p.Gln38Ter Single submitter Inborn genetic diseases
- p.Ile106Leu Single submitter Inborn genetic diseases ⚠
- p.Ile109Leu Single submitter Inborn genetic diseases ⚠
- p.Leu63Pro Single submitter ⚠
- p.Lys59del Single submitter neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements
- p.Lys94Gln Single submitter Inborn genetic diseases ⚠
- p.Pro9Leu Single submitter ⚠
- p.Val53Ile Single submitter ⚠