PDCD10 — 189 ClinVar variants
All ClinVar germline PDCD10 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 39 flagged for review →
53 Pathogenic · 7 Pathogenic/Likely pathogenic · 19 Likely pathogenic · 1 Conflicting · 14 Benign · 2 Benign/Likely benign · 31 Likely benign · 62 Uncertain significance
Full PDCD10 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 39
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 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
PDCD10 p.Val192Ile
Conflicting
Single submitter
cerebral cavernous malformation 3
Predictors lean, ClinVar uncertain 28
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
PDCD10 p.Arg196Gln
Uncertain significance
Multiple submitters
cerebral cavernous malformation 3
-
PDCD10 p.Asn104Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PDCD10 p.Leu44Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PDCD10 p.Met20Val
Uncertain significance
Multiple submitters
cerebral cavernous malformation 3
-
PDCD10 p.Phe76Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PDCD10 p.Val72Met
Uncertain significance
Multiple submitters
cerebral cavernous malformation 3
-
PDCD10 p.Ala135Asp
Uncertain significance
Single submitter
cerebral cavernous malformation 3
- PDCD10 p.Ala212Ser Uncertain significance Single submitter
-
PDCD10 p.Ala24Val
Uncertain significance
Single submitter
cerebral cavernous malformation 3
-
PDCD10 p.Arg35Gln
Uncertain significance
Single submitter
cerebral cavernous malformation 3
- PDCD10 p.Arg82Cys Uncertain significance Single submitter
- PDCD10 p.Asn147Asp Uncertain significance Single submitter
- PDCD10 p.Gln101Arg Uncertain significance Single submitter
-
PDCD10 p.Gln112Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Glu105Lys
Uncertain significance
Single submitter
Inborn genetic diseases
- PDCD10 p.Ile134Thr Uncertain significance Single submitter
-
PDCD10 p.Leu178Pro
Uncertain significance
Single submitter
cerebral cavernous malformation 3
- PDCD10 p.Leu197Pro Uncertain significance Single submitter
-
PDCD10 p.Leu44Pro
Uncertain significance
Single submitter
cerebral cavernous malformation 3
- PDCD10 p.Leu58Pro Uncertain significance Single submitter
-
PDCD10 p.Lys172Thr
Uncertain significance
Single submitter
Inborn genetic diseases
- PDCD10 p.Lys179Glu Uncertain significance Single submitter
-
PDCD10 p.Lys186Arg
Uncertain significance
Single submitter
cerebral cavernous malformation 3
-
PDCD10 p.Lys65Gln
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Ser71Asn
Uncertain significance
Single submitter
cerebral cavernous malformation 3
-
PDCD10 p.Ser71Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Thr77Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Met26Arg
Uncertain significance
No assertion criteria
cerebral cavernous malformation 3
Predictors split 10
The independent predictors disagree with each other — read with care.
-
PDCD10 p.Arg126Met
Uncertain significance
Multiple submitters
cerebral cavernous malformation 3
-
PDCD10 p.Tyr27Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PDCD10 p.Arg158Ser Uncertain significance Single submitter
-
PDCD10 p.Asn156Lys
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Asp133Ala
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Ile138Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Phe191Ile
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Tyr181Cys
Uncertain significance
Single submitter
cerebral cavernous malformation 3
-
PDCD10 p.Tyr23Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
PDCD10 p.Tyr91His
Uncertain significance
Single submitter
cerebral cavernous malformation 3
All PDCD10 variants
Pathogenic 53
- c.268+1G>A Multiple submitters
- c.396-2A>G Multiple submitters cerebral cavernous malformation 3
- c.557+1G>A Multiple submitters cerebral cavernous malformation 3
- p.Arg108Ter Multiple submitters cerebral cavernous malformation 3
- p.Arg124fs Multiple submitters PDCD10-related disorder
- p.Arg196Ter Multiple submitters PDCD10-related disorder
- p.Arg35Ter Multiple submitters cerebral cavernous malformation 3
- p.Arg95Ter Multiple submitters PDCD10-related disorder
- p.Gln112fs Multiple submitters cerebral cavernous malformation 3
- p.Glu140Ter Multiple submitters cerebral cavernous malformation 3
- p.Lys70Ter Multiple submitters cerebral cavernous malformation 3
- p.Ser71fs Multiple submitters cerebral cavernous malformation 3
- c.395+1G>C Single submitter
- c.395+2T>G Single submitter
- c.396-2A>C Single submitter cerebral cavernous malformation 3
- c.396-3C>G Single submitter
- c.475-1G>A Single submitter cerebral cavernous malformation 3
- c.557+1G>T Single submitter cerebral cavernous malformation 3
- c.558-1G>A Single submitter cerebral cavernous malformation 3
- c.558-2A>C Single submitter cerebral cavernous malformation 3
- c.558-2A>G Single submitter cerebral cavernous malformation 3
- c.97-1G>A Single submitter cerebral cavernous malformation 3
- c.-117+6518_20del Single submitter cerebral cavernous malformation 3
- p.Arg45fs Single submitter cerebral cavernous malformation 1
- p.Arg82fs Single submitter cerebral cavernous malformation 3
- p.Asn156fs Single submitter
- p.Asn55fs Single submitter cerebral cavernous malformation 3
- p.Gln101Ter Single submitter cerebral cavernous malformation 3
- p.Gln60Ter Single submitter cerebral cavernous malformation 3
- p.Glu166fs Single submitter cerebral cavernous malformation 3
- p.Glu52fs Single submitter cerebral cavernous malformation 3
- p.Glu54fs Single submitter cerebral cavernous malformation 3
- p.Glu54Ter Single submitter cerebral cavernous malformation 3
- p.Ile131fs Single submitter cerebral cavernous malformation 3
- p.Ile198fs Single submitter cerebral cavernous malformation 3
- p.Leu38fs Single submitter PDCD10-related disorder
- p.Leu44_Arg45insTer Single submitter cerebral cavernous malformation 3
- p.Lys111fs Single submitter cerebral cavernous malformation 3
- p.Lys132Ter Single submitter cerebral cavernous malformation 3
- p.Lys164fs Single submitter cerebral cavernous malformation 3
- p.Met92fs Single submitter cerebral cavernous malformation 3
- p.Phe100fs Single submitter Inborn genetic diseases
- p.Phe174fs Single submitter cerebral cavernous malformation 3
- p.Pro21fs Single submitter cerebral cavernous malformation 3
- p.Ser16fs Single submitter cerebral cavernous malformation 3
- p.Ser193fs Single submitter cerebral cavernous malformation 3
- p.Thr130fs Single submitter cerebral cavernous malformation 3
- p.Thr144fs Single submitter cerebral cavernous malformation 3
- p.Thr77fs Single submitter cerebral cavernous malformation 3
- p.Tyr23fs Single submitter cerebral cavernous malformation 3
- p.Val148fs Single submitter cerebral cavernous malformation 3
- c.97_150del No assertion criteria cerebral cavernous malformation 3
- p.Gln129Ter No assertion criteria cerebral cavernous malformation 3
Pathogenic/Likely pathogenic 7
- c.150+1G>A Multiple submitters
- c.474+5G>A Multiple submitters arteriovenous malformations of the brain
- c.557+4_557+7del Multiple submitters cerebral cavernous malformation 3
- p.Asn195fs Multiple submitters cerebral cavernous malformation 3
- p.Thr177fs Multiple submitters cerebral cavernous malformation 3
- p.Tyr152Ter Multiple submitters cerebral cavernous malformation 3
- p.Tyr170Ter Multiple submitters cerebral cavernous malformation 3
Likely pathogenic 19
- c.269_270delAG Multiple submitters
- c.150+1G>T Single submitter
- c.268+1del Single submitter
- c.268+2T>A Single submitter PDCD10-related disorder
- c.269-1G>C Single submitter cerebral cavernous malformation 3
- c.395+1G>A Single submitter
- c.396-2A>T Single submitter
- c.474+1dup Single submitter PDCD10-related disorder
- c.558-2A>T Single submitter
- p.Ala40fs Single submitter
- p.Asn104fs Single submitter PDCD10-related disorder
- p.Asn189fs Single submitter PDCD10-related disorder
- p.Asn37fs Single submitter PDCD10-related disorder
- p.Gln200Ter Single submitter
- p.Glu166Ter Single submitter
- p.Ile131Ser Single submitter
- p.Met26fs Single submitter cerebral cavernous malformation 3
- p.Phe167fs Single submitter
- p.Tyr154Ter Single submitter PDCD10-related disorder
Conflicting classifications of pathogenicity 1
- p.Val192Ile Single submitter cerebral cavernous malformation 3 ⚠
Benign 14
- c.150+93G>A Multiple submitters
- c.558-59A>G Multiple submitters
- c.558-97T>C Multiple submitters
- c.-116-9T>C Multiple submitters cerebral cavernous malformation 3
- c.-1226C>T Multiple submitters cerebral cavernous malformation 3
- c.150+273dup Single submitter
- c.150+285del Single submitter
- c.151-14del Single submitter cerebral cavernous malformation 3
- c.269-260del Single submitter
- c.269-277del Single submitter
- c.395+203_395+205del Single submitter
- c.395+216A>G Single submitter
- c.475-11del Single submitter cerebral cavernous malformation 3
- c.558-267T>G Single submitter
Benign/Likely benign 2
- c.474+9A>G Multiple submitters cerebral cavernous malformation 3
- p.Val72Leu Multiple submitters Inborn genetic diseases
Likely benign 31
- p.Ala46= Multiple submitters Inborn genetic diseases
- p.Phe127= Multiple submitters Inborn genetic diseases
- p.Phe191= Multiple submitters cerebral cavernous malformation 3
- p.Phe76= Multiple submitters cerebral cavernous malformation 3
- c.150+11A>G Single submitter cerebral cavernous malformation 3
- c.151-7A>G Single submitter cerebral cavernous malformation 3
- c.268+18del Single submitter cerebral cavernous malformation 3
- c.269-16G>A Single submitter cerebral cavernous malformation 3
- c.395+46C>T Single submitter cerebral cavernous malformation 3
- c.396-19T>C Single submitter cerebral cavernous malformation 3
- c.475-20A>C Single submitter
- c.475-4del Single submitter cerebral cavernous malformation 3
- c.475-8G>A Single submitter cerebral cavernous malformation 3
- c.96+17T>C Single submitter cerebral cavernous malformation 3
- c.-284C>T Single submitter
- c.*285G>T Single submitter cerebral cavernous malformation 3
- p.Ala24= Single submitter cerebral cavernous malformation 3
- p.Arg126= Single submitter Inborn genetic diseases
- p.Arg2= Single submitter Inborn genetic diseases
- p.Asn104= Single submitter cerebral cavernous malformation 3
- p.Gln129= Single submitter cerebral cavernous malformation 3
- p.Glu90= Single submitter cerebral cavernous malformation 3
- p.Leu22= Single submitter cerebral cavernous malformation 3
- p.Leu33= Single submitter Inborn genetic diseases
- p.Lys165= Single submitter Inborn genetic diseases
- p.Lys53= Single submitter cerebral cavernous malformation 3
- p.Lys65= Single submitter Inborn genetic diseases
- p.Pro118= Single submitter cerebral cavernous malformation 3
- p.Ser71= Single submitter cerebral cavernous malformation 3
- p.Thr15= Single submitter cerebral cavernous malformation 3
- p.Thr210= Single submitter Inborn genetic diseases
Uncertain significance 62
- c.*199A>C Multiple submitters cerebral cavernous malformation 3
- c.*339G>A Multiple submitters cerebral cavernous malformation 3
- p.Arg126Met Multiple submitters cerebral cavernous malformation 3 ⚠
- p.Arg196Gln Multiple submitters cerebral cavernous malformation 3 ⚠
- p.Asn104Ser Multiple submitters Inborn genetic diseases ⚠
- p.Leu44Arg Multiple submitters Inborn genetic diseases ⚠
- p.Met20Val Multiple submitters cerebral cavernous malformation 3 ⚠
- p.Phe76Val Multiple submitters Inborn genetic diseases ⚠
- p.Tyr27Cys Multiple submitters Inborn genetic diseases ⚠
- p.Val72Met Multiple submitters cerebral cavernous malformation 3 ⚠
- c.151-11C>T Single submitter cerebral cavernous malformation 3
- c.268+3A>G Single submitter
- c.268+5C>G Single submitter cerebral cavernous malformation 3
- c.268+6G>A Single submitter cerebral cavernous malformation 3
- c.474+4_474+5insACAA Single submitter cerebral cavernous malformation 3
- c.474+4C>A Single submitter cerebral cavernous malformation 3
- c.558-3C>G Single submitter
- c.-15G>A Single submitter
- c.*139A>G Single submitter cerebral cavernous malformation 3
- c.*141C>T Single submitter cerebral cavernous malformation 3
- c.*174C>T Single submitter cerebral cavernous malformation 3
- c.*221T>C Single submitter cerebral cavernous malformation 3
- c.*63T>C Single submitter cerebral cavernous malformation 3
- c.*87A>T Single submitter cerebral cavernous malformation 3
- p.Ala135Asp Single submitter cerebral cavernous malformation 3 ⚠
- p.Ala212Ser Single submitter ⚠
- p.Ala24_Pro28del Single submitter cerebral cavernous malformation 3
- p.Ala24Val Single submitter cerebral cavernous malformation 3 ⚠
- p.Ala85Val Single submitter
- p.Arg158Ser Single submitter ⚠
- p.Arg35Gln Single submitter cerebral cavernous malformation 3 ⚠
- p.Arg82Cys Single submitter ⚠
- p.Asn147Asp Single submitter ⚠
- p.Asn156Lys Single submitter Inborn genetic diseases ⚠
- p.Asp133Ala Single submitter Inborn genetic diseases ⚠
- p.Gln101Arg Single submitter ⚠
- p.Gln112Arg Single submitter Inborn genetic diseases ⚠
- p.Glu105Lys Single submitter Inborn genetic diseases ⚠
- p.Glu140_Leu142del Single submitter cerebral cavernous malformation 3
- p.Ile134Thr Single submitter ⚠
- p.Ile138Met Single submitter Inborn genetic diseases ⚠
- p.Ile49del Single submitter cerebral cavernous malformation 3
- p.Ile63del Single submitter
- p.Leu178Pro Single submitter cerebral cavernous malformation 3 ⚠
- p.Leu197_Ile198insLys Single submitter
- p.Leu197Pro Single submitter ⚠
- p.Leu44Pro Single submitter cerebral cavernous malformation 3 ⚠
- p.Leu58Pro Single submitter ⚠
- p.Lys172Thr Single submitter Inborn genetic diseases ⚠
- p.Lys179Glu Single submitter ⚠
- p.Lys186Arg Single submitter cerebral cavernous malformation 3 ⚠
- p.Lys65Gln Single submitter Inborn genetic diseases ⚠
- p.Met8del Single submitter
- p.Phe191Ile Single submitter Inborn genetic diseases ⚠
- p.Ser71Asn Single submitter cerebral cavernous malformation 3 ⚠
- p.Ser71Gly Single submitter Inborn genetic diseases ⚠
- p.Thr77Met Single submitter Inborn genetic diseases ⚠
- p.Tyr181Cys Single submitter cerebral cavernous malformation 3 ⚠
- p.Tyr23Cys Single submitter Inborn genetic diseases ⚠
- p.Tyr91His Single submitter cerebral cavernous malformation 3 ⚠
- p.Lys50= No assertion criteria PDCD10-related disorder
- p.Met26Arg No assertion criteria cerebral cavernous malformation 3 ⚠