VPS50 — 114 ClinVar variants

All ClinVar germline VPS50 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 85 flagged for review →

3 Pathogenic · 5 Likely pathogenic · 2 Benign · 14 Likely benign · 90 Uncertain significance

Full VPS50 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 85

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 72

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

Predictors split 13

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

All VPS50 variants

Pathogenic 3

c.1978-1G>T No assertion criteria neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
p.Lys5Ter No assertion criteria neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
p.Thr608del No assertion criteria neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis

Likely pathogenic 5

c.2208-2A>G Single submitter
c.2464-1G>C Single submitter
p.Arg569Ter Single submitter neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
p.Gln575Ter Single submitter neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
p.Pro580fs Single submitter

Benign 2

p.Asn865Ser Multiple submitters
p.Pro896= Multiple submitters

Likely benign 14

p.Asn529Tyr Multiple submitters
c.225+15A>G Single submitter
c.2463+10C>T Single submitter
p.Ala326= Single submitter
p.Ala773Thr Single submitter
p.Ala88Glu Single submitter
p.Leu647= Single submitter
p.Phe414= Single submitter
p.Pro779= Single submitter
p.Thr284= Single submitter
p.Thr397= Single submitter
p.Thr663= Single submitter
p.Tyr863= Single submitter
p.Tyr910= Single submitter

Uncertain significance 90

p.Glu700Lys Multiple submitters ⚠
c.102+2T>G Single submitter
c.1361+1G>T Single submitter
p.Ala153Asp Single submitter ⚠
p.Ala357Pro Single submitter ⚠
p.Arg164Cys Single submitter ⚠
p.Arg164His Single submitter
p.Arg182Thr Single submitter
p.Arg30Gln Single submitter ⚠
p.Arg30Trp Single submitter ⚠
p.Arg373Cys Single submitter ⚠
p.Arg38Gly Single submitter ⚠
p.Arg41Gln Single submitter ⚠
p.Arg493His Single submitter ⚠
p.Arg586Gln Single submitter neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis ⚠
p.Arg656Gln Single submitter ⚠
p.Arg702Gly Single submitter ⚠
p.Arg777Gln Single submitter ⚠
p.Arg874His Single submitter ⚠
p.Asn362Asp Single submitter ⚠
p.Asn677Ser Single submitter ⚠
p.Asn856Ser Single submitter ⚠
p.Asp195Asn Single submitter
p.Asp195Gly Single submitter ⚠
p.Asp22His Single submitter ⚠
p.Asp353His Single submitter ⚠
p.Asp547Gly Single submitter ⚠
p.Cys296Tyr Single submitter ⚠
p.Gln305Lys Single submitter ⚠
p.Gln793His Single submitter ⚠
p.Glu120Gly Single submitter ⚠
p.Glu234Ala Single submitter ⚠
p.Glu368Lys Single submitter ⚠
p.Glu428Asp Single submitter ⚠
p.Glu428Gln Single submitter ⚠
p.Glu849Asp Single submitter ⚠
p.Gly873Ser Single submitter ⚠
p.His453Arg Single submitter ⚠
p.His484Tyr Single submitter ⚠
p.His943Leu Single submitter ⚠
p.Ile108Val Single submitter ⚠
p.Ile406Val Single submitter ⚠
p.Ile418Val Single submitter ⚠
p.Ile606Val Single submitter ⚠
p.Ile615Val Single submitter ⚠
p.Ile894Val Single submitter ⚠
p.Ile897Thr Single submitter ⚠
p.Leu143Phe Single submitter ⚠
p.Leu20Phe Single submitter ⚠
p.Leu337His Single submitter ⚠
p.Leu667Phe Single submitter ⚠
p.Lys963Arg Single submitter ⚠
p.Lys963Gln Single submitter ⚠
p.Met270Val Single submitter ⚠
p.Met343Val Single submitter ⚠
p.Met363Val Single submitter ⚠
p.Met639Lys Single submitter ⚠
p.Met886Val Single submitter neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis ⚠
p.Phe514Ser Single submitter ⚠
p.Pro564Leu Single submitter ⚠
p.Pro78Leu Single submitter ⚠
p.Pro898Leu Single submitter ⚠
p.Ser217Arg Single submitter ⚠
p.Ser21Thr Single submitter ⚠
p.Ser356Leu Single submitter ⚠
p.Ser361Ile Single submitter ⚠
p.Ser432Thr Single submitter ⚠
p.Ser479Asn Single submitter ⚠
p.Ser541Phe Single submitter ⚠
p.Ser585Tyr Single submitter ⚠
p.Ser591Ile Single submitter ⚠
p.Ser669Asn Single submitter ⚠
p.Thr151Ile Single submitter ⚠
p.Thr151Pro Single submitter ⚠
p.Thr354Ala Single submitter ⚠
p.Thr468Ala Single submitter ⚠
p.Thr512Asn Single submitter ⚠
p.Thr722Met Single submitter ⚠
p.Thr733Met Single submitter ⚠
p.Thr769Lys Single submitter ⚠
p.Thr929Ala Single submitter ⚠
p.Tyr260Cys Single submitter ⚠
p.Tyr557Cys Single submitter ⚠
p.Tyr781Cys Single submitter ⚠
p.Val104Met Single submitter ⚠
p.Val316Gly Single submitter ⚠
p.Val391Ile Single submitter ⚠
p.Val436Ile Single submitter ⚠
p.Val563Asp Single submitter ⚠
p.Val688Phe Single submitter ⚠