PDCD6IP — 109 ClinVar variants

All ClinVar germline PDCD6IP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 94 flagged for review →

1 Pathogenic · 2 Conflicting · 5 Benign · 5 Likely benign · 96 Uncertain significance

Full PDCD6IP gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 94

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 agree, ClinVar conflicts 2

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 70

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

Predictors split 22

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

All PDCD6IP variants

Pathogenic 1

p.Val54fs No assertion criteria microcephaly 29, primary, autosomal recessive

Conflicting classifications of pathogenicity 2

p.Ala719Thr Single submitter ⚠
p.Lys357Asn Single submitter ⚠

Benign 5

p.Gly429Ser Multiple submitters ⚠
p.Gly778Ala Multiple submitters
p.Pro749= Multiple submitters
p.Thr789= Multiple submitters
p.Val378Ile Single submitter

Likely benign 5

p.Ala726= Multiple submitters
c.2120+14G>A Single submitter
p.Gly811= Single submitter
p.Pro795Leu Single submitter
p.Ser770Pro Single submitter

Uncertain significance 96

p.Ala657Val Single submitter ⚠
p.Ala726Val Single submitter ⚠
p.Ala736Gly Single submitter ⚠
p.Ala798Val Single submitter ⚠
p.Ala825Val Single submitter ⚠
p.Arg422Gly Single submitter ⚠
p.Arg475Cys Single submitter ⚠
p.Arg56Cys Single submitter ⚠
p.Arg767Gln Single submitter ⚠
p.Asn305Ile Single submitter ⚠
p.Asn344His Single submitter ⚠
p.Asn494Ser Single submitter ⚠
p.Asn531Ser Single submitter ⚠
p.Asn571Ser Single submitter ⚠
p.Asn662Ser Single submitter ⚠
p.Asn678Ser Single submitter ⚠
p.Asp100Asn Single submitter ⚠
p.Asp299Glu Single submitter ⚠
p.Asp314Asn Single submitter ⚠
p.Asp316Asn Single submitter ⚠
p.Asp465Asn Single submitter ⚠
p.Asp467Gly Single submitter ⚠
p.Asp591Gly Single submitter
p.Asp59Ala Single submitter ⚠
p.Cys524Ser Single submitter ⚠
p.Gln27Glu Single submitter ⚠
p.Gln36Lys Single submitter ⚠
p.Gln427Arg Single submitter ⚠
p.Gln427Lys Single submitter ⚠
p.Gln508Arg Single submitter ⚠
p.Gln797Arg Single submitter ⚠
p.Glu272Asp Single submitter ⚠
p.Glu561Asp Single submitter ⚠
p.Glu603Gly Single submitter ⚠
p.Gly117Val Single submitter
p.Gly778Arg Single submitter ⚠
p.Gly848Glu Single submitter ⚠
p.His279Arg Single submitter ⚠
p.His838Gln Single submitter ⚠
p.Ile179Leu Single submitter ⚠
p.Ile212Leu Single submitter ⚠
p.Ile332Val Single submitter ⚠
p.Ile694Met Single submitter ⚠
p.Ile78Val Single submitter ⚠
p.Leu140Val Single submitter ⚠
p.Leu187Phe Single submitter
p.Leu201Phe Single submitter ⚠
p.Leu21Val Single submitter ⚠
p.Leu237Phe Single submitter ⚠
p.Leu326Phe Single submitter ⚠
p.Leu399Phe Single submitter ⚠
p.Leu65Ile Single submitter ⚠
p.Lys11Asn Single submitter ⚠
p.Lys285Asn Single submitter ⚠
p.Lys48Asn Single submitter ⚠
p.Lys614Glu Single submitter ⚠
p.Met252Thr Single submitter ⚠
p.Met358Ile Single submitter ⚠
p.Met358Thr Single submitter ⚠
p.Met819Val Single submitter ⚠
p.Phe242Leu Single submitter ⚠
p.Pro238Ala Single submitter ⚠
p.Pro331Ala Single submitter ⚠
p.Pro342Ser Single submitter ⚠
p.Pro346Ser Single submitter ⚠
p.Pro402Leu Single submitter ⚠
p.Pro441His Single submitter ⚠
p.Pro725Ala Single submitter ⚠
p.Pro731Ser Single submitter ⚠
p.Pro748Arg Single submitter ⚠
p.Pro748Leu Single submitter ⚠
p.Pro764Leu Single submitter ⚠
p.Pro790Leu Single submitter ⚠
p.Pro802His Single submitter ⚠
p.Pro845Leu Single submitter ⚠
p.Pro847Leu Single submitter ⚠
p.Pro852Leu Single submitter ⚠
p.Pro857Ala Single submitter ⚠
p.Ser188Arg Single submitter ⚠
p.Ser301Phe Single submitter ⚠
p.Ser423Tyr Single submitter ⚠
p.Thr236Ile Single submitter ⚠
p.Thr390Ser Single submitter ⚠
p.Thr741Pro Single submitter ⚠
p.Thr741Ser Single submitter ⚠
p.Tyr291Cys Single submitter
p.Tyr29Asp Single submitter ⚠
p.Tyr513Cys Single submitter
p.Tyr821Cys Single submitter ⚠
p.Tyr854Cys Single submitter ⚠
p.Tyr864Ser Single submitter ⚠
p.Val177Met Single submitter ⚠
p.Val424Leu Single submitter ⚠
p.Val503Met Single submitter ⚠
p.Val576Met Single submitter ⚠
p.Val777Leu Single submitter ⚠