TRAPPC2 — 156 ClinVar variants
All ClinVar germline TRAPPC2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 17 flagged for review →
26 Pathogenic · 2 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 3 Conflicting · 32 Benign · 3 Benign/Likely benign · 26 Likely benign · 55 Uncertain significance
Full TRAPPC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 17
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 14
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- TRAPPC2 p.Asn118Ser Uncertain significance Single submitter
- TRAPPC2 p.Glu92Asp Uncertain significance Single submitter
-
TRAPPC2 p.His137Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- TRAPPC2 p.His137Pro Uncertain significance Single submitter
- TRAPPC2 p.His137Tyr Uncertain significance Single submitter
- TRAPPC2 p.His13Arg Uncertain significance Single submitter
- TRAPPC2 p.His43Tyr Uncertain significance Single submitter
-
TRAPPC2 p.Met59Thr
Uncertain significance
Single submitter
spondyloepiphyseal dysplasia tarda
- TRAPPC2 p.Met85Leu Uncertain significance Single submitter
- TRAPPC2 p.Phe75Ile Uncertain significance Single submitter
- TRAPPC2 p.Thr63Ser Uncertain significance Single submitter
- TRAPPC2 p.Tyr6Cys Uncertain significance Single submitter
- TRAPPC2 p.Val49Ile Uncertain significance Single submitter
- TRAPPC2 p.Val76Ala Uncertain significance Single submitter
Predictors split 3
The independent predictors disagree with each other — read with care.
- TRAPPC2 p.Thr100Ile Uncertain significance Multiple submitters
-
TRAPPC2 p.Arg35His
Uncertain significance
Single submitter
Inborn genetic diseases
-
TRAPPC2 p.Glu69Gln
Uncertain significance
Single submitter
Inborn genetic diseases
All TRAPPC2 variants
Pathogenic 26
- c.93+5G>A Multiple submitters spondyloepiphyseal dysplasia tarda, X-linked
- p.Arg122Ter Multiple submitters
- p.Asp88fs Multiple submitters TRAPPC2-related disorder
- p.Gln91fs Multiple submitters hereditary spastic paraplegia 4
- p.Met81fs Multiple submitters TRAPPC2-related disorder
- p.Val64fs Multiple submitters spondyloepiphyseal dysplasia tarda
- c.239-1_239insTATTTCATA Single submitter
- c.324+1G>A Single submitter
- c.325-2A>G Single submitter
- p.Leu46fs Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- p.Phe109fs Single submitter
- p.Phe75fs Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- p.Phe7fs Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- p.Pro16fs Single submitter
- p.Ser73fs Single submitter spondyloepiphyseal dysplasia tarda
- p.Tyr106Ter Single submitter
- c.238+4T>C No assertion criteria spondyloepiphyseal dysplasia tarda
- c.239-11_239-9del No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Asp14fs No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Gln131Ter No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Lys31Ter No assertion criteria spondyloepiphyseal dysplasia tarda, X-linked
- p.Met1Leu No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Met53fs No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Ser110Ter No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Val130fs No assertion criteria spondyloepiphyseal dysplasia tarda
- p.Val17_Phe18insTer No assertion criteria spondyloepiphyseal dysplasia tarda
Pathogenic/Likely pathogenic 2
- c.325-1G>C Multiple submitters
- p.Ser73Leu Multiple submitters TRAPPC2-related disorder
Likely pathogenic 9
- c.239-20_239-12delinsAATGAA Multiple submitters spondyloepiphyseal dysplasia tarda, X-linked
- c.238+2T>C Single submitter
- c.93+1G>C Single submitter TRAPPC2-related disorder
- p.Arg128Ter Single submitter
- p.Gln131fs Single submitter spondyloepiphyseal dysplasia tarda
- p.His36fs Single submitter
- p.Phe83Ser Single submitter connective tissue disorder
- p.Val49fs Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- c.324+1G>T No assertion criteria spondyloepiphyseal dysplasia tarda
Conflicting classifications of pathogenicity 3
- c.239-10_239-7del Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- c.-97G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*263T>C Single submitter spondyloepiphyseal dysplasia tarda
Benign 32
- c.238+114A>G Multiple submitters
- c.*1052T>C Multiple submitters spondyloepiphyseal dysplasia tarda
- c.*1739C>G Multiple submitters spondyloepiphyseal dysplasia tarda
- c.*830G>C Multiple submitters spondyloepiphyseal dysplasia tarda
- c.325-270C>G Single submitter
- c.93+271G>A Single submitter
- c.93+61del Single submitter
- c.94-126_94-123dup Single submitter
- c.*1128C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*1436C>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*1443G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*1599T>C Single submitter spondyloepiphyseal dysplasia tarda
- c.*1634G>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*1963A>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*2035C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*262_*263dup Single submitter
- c.*263del Single submitter
- c.*263dup Single submitter
- c.*302A>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*393G>C Single submitter spondyloepiphyseal dysplasia tarda
- c.*394T>C Single submitter spondyloepiphyseal dysplasia tarda
- c.*490C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*546G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*641G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*709C>G Single submitter spondyloepiphyseal dysplasia tarda
- p.Ala78= Single submitter
- p.Asn38= Single submitter
- p.Asp32= Single submitter
- p.Ile89Val Single submitter
- p.Leu37= Single submitter
- p.Leu46= Single submitter
- p.Tyr103Cys Single submitter spondyloepiphyseal dysplasia tarda, X-linked
Benign/Likely benign 3
- c.239-20T>A Multiple submitters
- c.93+7A>G Multiple submitters spondyloepiphyseal dysplasia tarda
- p.Asn68= Multiple submitters
Likely benign 26
- c.238+134G>A Multiple submitters
- c.324+54T>G Multiple submitters
- c.-20+229G>A Multiple submitters
- c.*1229C>T Multiple submitters spondyloepiphyseal dysplasia tarda
- c.*29C>T Multiple submitters
- p.Phe109= Multiple submitters
- c.324+10G>A Single submitter
- c.324+15A>G Single submitter
- c.324+16T>C Single submitter
- c.325-12C>T Single submitter
- c.93+14T>C Single submitter
- c.94-6A>G Single submitter
- c.*1050C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*261_*263dup Single submitter
- c.*333G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*402C>T Single submitter
- c.*710T>C Single submitter spondyloepiphyseal dysplasia tarda
- c.*849C>T Single submitter spondyloepiphyseal dysplasia tarda
- p.His36= Single submitter
- p.His87= Single submitter
- p.Ile89= Single submitter
- p.Phe126Leu Single submitter
- p.Pro117= Single submitter
- p.Pro16= Single submitter
- p.Thr63= Single submitter
- p.Val17= Single submitter
Uncertain significance 55
- c.*1436C>T Multiple submitters spondyloepiphyseal dysplasia tarda
- c.*942G>T Multiple submitters spondyloepiphyseal dysplasia tarda
- p.Thr100Ile Multiple submitters ⚠
- c.239-14_239-12del Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- c.93+4C>T Single submitter
- c.-19-2_-19delinsGGA Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- c.-19-2A>T Single submitter
- c.-19-3T>C Single submitter spondyloepiphyseal dysplasia tarda
- c.-19G>T Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- c.*1032T>C Single submitter spondyloepiphyseal dysplasia tarda
- c.*1191C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*1287G>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*1288T>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*1442C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*1486G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*179A>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*187A>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*2060G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*243G>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*308G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*323T>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*332C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*435A>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*465T>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*522G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*670C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*690T>C Single submitter spondyloepiphyseal dysplasia tarda
- c.*703G>A Single submitter spondyloepiphyseal dysplasia tarda
- c.*712A>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*752A>G Single submitter spondyloepiphyseal dysplasia tarda
- c.*867C>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*949G>T Single submitter spondyloepiphyseal dysplasia tarda
- c.*950_*956dup Single submitter
- c.*989G>T Single submitter spondyloepiphyseal dysplasia tarda
- p.Arg35His Single submitter Inborn genetic diseases ⚠
- p.Asn118fs Single submitter spondyloepiphyseal dysplasia tarda, X-linked
- p.Asn118Ser Single submitter ⚠
- p.Glu69Gln Single submitter Inborn genetic diseases ⚠
- p.Glu92Asp Single submitter ⚠
- p.His137Arg Single submitter Inborn genetic diseases ⚠
- p.His137Pro Single submitter ⚠
- p.His137Tyr Single submitter ⚠
- p.His13Arg Single submitter ⚠
- p.His43Tyr Single submitter ⚠
- p.Leu48= Single submitter
- p.Met59Thr Single submitter spondyloepiphyseal dysplasia tarda ⚠
- p.Met85Leu Single submitter ⚠
- p.Phe75Ile Single submitter ⚠
- p.Phe99del Single submitter
- p.Ter141Cys Single submitter
- p.Thr63Ser Single submitter ⚠
- p.Tyr6Cys Single submitter ⚠
- p.Val49Ile Single submitter ⚠
- p.Val76Ala Single submitter ⚠
- p.Val8Ile Single submitter Inborn genetic diseases