PCYT1A — 263 ClinVar variants
All ClinVar germline PCYT1A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 106 flagged for review →
5 Pathogenic · 1 Pathogenic/Likely pathogenic · 7 Likely pathogenic · 12 Conflicting · 7 Benign · 8 Benign/Likely benign · 104 Likely benign · 119 Uncertain significance
Full PCYT1A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 106
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 4
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
PCYT1A p.Arg328His
Conflicting
Single submitter
inherited retinal dystrophy
- PCYT1A p.Arg335Gln Conflicting Single submitter
-
PCYT1A p.Asn236Ser
Conflicting
Single submitter
Inborn genetic diseases
- PCYT1A p.Pro330Ser Conflicting Single submitter
Predictors lean, ClinVar uncertain 76
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
PCYT1A p.Ala18Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PCYT1A p.Ala217Val Uncertain significance Multiple submitters
- PCYT1A p.Arg211Trp Uncertain significance Multiple submitters
-
PCYT1A p.Arg326Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Arg326His
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Arg328Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Arg75Gln
Uncertain significance
Multiple submitters
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- PCYT1A p.Asp179Val Uncertain significance Multiple submitters
-
PCYT1A p.Asp360Gly
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Cys5Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Glu291Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PCYT1A p.Gly29Arg Uncertain significance Multiple submitters
- PCYT1A p.Gly340Ser Uncertain significance Multiple submitters
- PCYT1A p.Lys186Glu Uncertain significance Multiple submitters
-
PCYT1A p.Pro19Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PCYT1A p.Pro21Ser Uncertain significance Multiple submitters
- PCYT1A p.Pro320Ser Uncertain significance Multiple submitters
-
PCYT1A p.Pro330Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PCYT1A p.Pro332Ser Uncertain significance Multiple submitters
- PCYT1A p.Pro344Ser Uncertain significance Multiple submitters
-
PCYT1A p.Pro348Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Pro348Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Ser315Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Thr25Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Val30Ile
Uncertain significance
Multiple submitters
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
-
PCYT1A p.Ala349Val
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Ala3Glu Uncertain significance Single submitter
-
PCYT1A p.Ala93Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Arg219Trp Uncertain significance Single submitter
- PCYT1A p.Arg309Gln Uncertain significance Single submitter
- PCYT1A p.Arg309Pro Uncertain significance Single submitter
- PCYT1A p.Arg326Leu Uncertain significance Single submitter
- PCYT1A p.Arg335Pro Uncertain significance Single submitter
- PCYT1A p.Arg36His Uncertain significance Single submitter
- PCYT1A p.Arg42Gln Uncertain significance Single submitter
- PCYT1A p.Arg61Gly Uncertain significance Single submitter
-
PCYT1A p.Arg75Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Arg94Gln Uncertain significance Single submitter
- PCYT1A p.Asn350Lys Uncertain significance Single submitter
- PCYT1A p.Asn350Ser Uncertain significance Single submitter
- PCYT1A p.Asp28Gly Uncertain significance Single submitter
- PCYT1A p.Asp367Asn Uncertain significance Single submitter
-
PCYT1A p.Cys37Tyr
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Cys5Tyr Uncertain significance Single submitter
-
PCYT1A p.Glu17Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Glu327Gly Uncertain significance Single submitter
-
PCYT1A p.Gly199Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Gly20Arg Uncertain significance Single submitter
-
PCYT1A p.His241Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.His354Gln Uncertain significance Single submitter
- PCYT1A p.His354Tyr Uncertain significance Single submitter
- PCYT1A p.Ile200Val Uncertain significance Single submitter
- PCYT1A p.Ile286Thr Uncertain significance Single submitter
- PCYT1A p.Leu311Pro Uncertain significance Single submitter
- PCYT1A p.Leu351Phe Uncertain significance Single submitter
- PCYT1A p.Lys100Asn Uncertain significance Single submitter
- PCYT1A p.Lys259Arg Uncertain significance Single submitter
- PCYT1A p.Lys277Arg Uncertain significance Single submitter
- PCYT1A p.Lys281Arg Uncertain significance Single submitter
- PCYT1A p.Lys341Arg Uncertain significance Single submitter
- PCYT1A p.Lys8Gln Uncertain significance Single submitter
- PCYT1A p.Pro31Leu Uncertain significance Single submitter
- PCYT1A p.Pro44Arg Uncertain significance Single submitter
- PCYT1A p.Pro44Ser Uncertain significance Single submitter
- PCYT1A p.Ser322Gly Uncertain significance Single submitter
- PCYT1A p.Ser333Pro Uncertain significance Single submitter
- PCYT1A p.Ser347Pro Uncertain significance Single submitter
-
PCYT1A p.Thr106Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
PCYT1A p.Thr25Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Thr342Ala Uncertain significance Single submitter
-
PCYT1A p.Tyr240Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
PCYT1A p.Tyr359Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Tyr59Ser Uncertain significance Single submitter
- PCYT1A p.Val30Phe Uncertain significance Single submitter
- PCYT1A p.Ala93Thr Uncertain significance No assertion criteria
-
PCYT1A p.Leu41Val
Uncertain significance
No assertion criteria
inherited retinal dystrophy
Predictors split 26
The independent predictors disagree with each other — read with care.
-
PCYT1A p.Ile109Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PCYT1A p.Pro295Leu Uncertain significance Multiple submitters
-
PCYT1A p.Pro46Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
PCYT1A p.Tyr59Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
- PCYT1A p.Ala313Thr Uncertain significance Single submitter
- PCYT1A p.Ala313Val Conflicting Single submitter
- PCYT1A p.Ala67Gly Uncertain significance Single submitter
-
PCYT1A p.Arg12Ser
Uncertain significance
Single submitter
lipodystrophy, congenital generalized, type 5
- PCYT1A p.Arg245Ser Uncertain significance Single submitter
- PCYT1A p.Arg283Gln Uncertain significance Single submitter
-
PCYT1A p.Asp170Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Glu65Gly Uncertain significance Single submitter
- PCYT1A p.Gly297Arg Uncertain significance Single submitter
- PCYT1A p.Leu102Val Uncertain significance Single submitter
- PCYT1A p.Lys100Arg Uncertain significance Single submitter
-
PCYT1A p.Phe285Tyr
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Pro316Leu Uncertain significance Single submitter
- PCYT1A p.Pro72Thr Uncertain significance Single submitter
- PCYT1A p.Ser315Asn Uncertain significance Single submitter
- PCYT1A p.Ser315Gly Uncertain significance Single submitter
-
PCYT1A p.Ser90Pro
Uncertain significance
Single submitter
Inborn genetic diseases
- PCYT1A p.Thr207Ile Uncertain significance Single submitter
- PCYT1A p.Trp336Arg Uncertain significance Single submitter
- PCYT1A p.Val267Ala Uncertain significance Single submitter
- PCYT1A p.Val267Met Uncertain significance Single submitter
- PCYT1A p.Val79Ile Uncertain significance Single submitter
All PCYT1A variants
Pathogenic 5
- p.Ala99Val Multiple submitters Inborn genetic diseases
- p.Arg75Ter Multiple submitters spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Ala99Thr Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Glu284Ter Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Phe191Leu Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
Pathogenic/Likely pathogenic 1
- p.Arg223Ser Multiple submitters spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
Likely pathogenic 7
- c.-10-2A>T Multiple submitters PCYT1A-related disorders
- c.708+1G>A Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- c.-10-2A>G Single submitter PCYT1A-related disorders
- p.Ala313fs Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Gln243Ter Single submitter PCYT1A-related disorders
- p.Pro21fs Single submitter
- p.Ser319fs Single submitter
Conflicting classifications of pathogenicity 12
- c.897+16C>G Single submitter
- p.Ala313Val Single submitter ⚠
- p.Arg208Ter Single submitter PCYT1A-related disorders
- p.Arg283Ter Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Arg328His Single submitter inherited retinal dystrophy ⚠
- p.Arg335Gln Single submitter ⚠
- p.Arg94Ter Single submitter PCYT1A-related disorders
- p.Asn236Ser Single submitter Inborn genetic diseases ⚠
- p.Glu280del Single submitter lipodystrophy, congenital generalized, type 5
- p.Pro330Ser Single submitter ⚠
- p.Ser323fs Single submitter spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Ser331fs Single submitter PCYT1A-related disorders
Benign 7
- c.218-90G>C Multiple submitters
- c.334+142A>T Multiple submitters
- c.566-225C>T Multiple submitters
- c.708+176C>T Multiple submitters
- c.897+160C>T Multiple submitters
- c.*50A>G Multiple submitters
- p.His301= Multiple submitters
Benign/Likely benign 8
- c.118-6C>T Multiple submitters
- c.897+12C>T Multiple submitters
- p.Ala81= Multiple submitters
- p.Arg36Cys Multiple submitters
- p.Arg42Trp Multiple submitters
- p.Pro332= Multiple submitters
- p.Ser339= Multiple submitters
- p.Ser347= Multiple submitters
Likely benign 104
- c.218-20A>G Multiple submitters
- c.565+12G>C Multiple submitters
- c.897+13C>T Multiple submitters
- c.898-12C>G Multiple submitters
- c.898-12C>T Multiple submitters
- p.Ala99= Multiple submitters
- p.Arg328= Multiple submitters
- p.Asn10= Multiple submitters
- p.Asn22= Multiple submitters
- p.Gly297= Multiple submitters
- p.Gly308= Multiple submitters
- p.His92= Multiple submitters
- p.Leu221= Multiple submitters
- p.Lys281= Multiple submitters
- p.Pro19= Multiple submitters
- p.Pro21= Multiple submitters
- p.Pro316= Multiple submitters
- p.Pro320= Multiple submitters
- p.Pro330= Multiple submitters
- p.Pro337Leu Multiple submitters
- p.Pro337Ser Multiple submitters
- p.Ser315= Multiple submitters
- p.Ser319= Multiple submitters
- p.Ser323= Multiple submitters
- p.Ser68= Multiple submitters
- p.Thr106= Multiple submitters
- p.Thr325Ala Multiple submitters Inborn genetic diseases
- p.Tyr359= Multiple submitters
- p.Val264= Multiple submitters
- c.117+12T>C Single submitter
- c.117+16C>T Single submitter
- c.117+9A>C Single submitter
- c.118-10A>G Single submitter
- c.118-11C>T Single submitter
- c.118-4T>C Single submitter
- c.217+12C>T Single submitter
- c.217+16_217+18del Single submitter
- c.218-12A>G Single submitter
- c.218-14T>C Single submitter
- c.218-18T>G Single submitter
- c.334+13T>C Single submitter
- c.487-11C>G Single submitter
- c.487-20T>C Single submitter
- c.565+20T>C Single submitter
- c.565+7G>A Single submitter
- c.566-13G>A Single submitter
- c.566-15G>A Single submitter
- c.566-17A>G Single submitter
- c.566-4T>G Single submitter
- c.566-6A>C Single submitter
- c.708+10A>G Single submitter
- c.708+14_708+17dup Single submitter
- c.708+14T>G Single submitter
- c.708+17C>T Single submitter
- c.708+8C>G Single submitter
- c.709-13T>C Single submitter
- c.897+8C>A Single submitter
- c.897+8C>G Single submitter
- c.898-11G>C Single submitter
- c.898-11G>T Single submitter
- c.898-16C>G Single submitter
- c.-10-3C>T Single submitter
- c.-10-4C>T Single submitter
- p.Ala11= Single submitter
- p.Ala18= Single submitter
- p.Ala217= Single submitter
- p.Ala313= Single submitter
- p.Ala349= Single submitter
- p.Ala7= Single submitter
- p.Arg12= Single submitter
- p.Arg196= Single submitter
- p.Arg326= Single submitter
- p.Arg61= Single submitter
- p.Asp273= Single submitter
- p.Asp364Val Single submitter
- p.Cys73= Single submitter
- p.Glu280= Single submitter
- p.Glu327= Single submitter
- p.Glu327Lys Single submitter
- p.Glu52= Single submitter
- p.Gly177= Single submitter
- p.Gly224= Single submitter
- p.Gly91= Single submitter
- p.His89= Single submitter
- p.Ile109= Single submitter
- p.Ile163= Single submitter
- p.Ile205= Single submitter
- p.Ile206= Single submitter
- p.Leu108= Single submitter
- p.Leu230= Single submitter
- p.Leu299= Single submitter
- p.Lys277= Single submitter
- p.Phe285= Single submitter
- p.Pro295= Single submitter
- p.Pro345= Single submitter
- p.Pro348= Single submitter
- p.Ser271= Single submitter
- p.Ser322= Single submitter
- p.Ser331= Single submitter
- p.Ser352= Single submitter
- p.Thr207= Single submitter
- p.Thr25= Single submitter
- p.Val210= Single submitter
- p.Val267= Single submitter
Uncertain significance 119
- c.117+5G>A Multiple submitters inherited retinal dystrophy
- p.Ala18Val Multiple submitters Inborn genetic diseases ⚠
- p.Ala217Val Multiple submitters ⚠
- p.Arg211Trp Multiple submitters ⚠
- p.Arg326Cys Multiple submitters Inborn genetic diseases ⚠
- p.Arg326His Multiple submitters Inborn genetic diseases ⚠
- p.Arg328Cys Multiple submitters Inborn genetic diseases ⚠
- p.Arg335Ter Multiple submitters
- p.Arg75Gln Multiple submitters spondylometaphyseal dysplasia-cone-rod dystrophy syndrome ⚠
- p.Asp179Val Multiple submitters ⚠
- p.Asp360Gly Multiple submitters Inborn genetic diseases ⚠
- p.Cys5Arg Multiple submitters Inborn genetic diseases ⚠
- p.Glu291Gln Multiple submitters Inborn genetic diseases ⚠
- p.Gly29Arg Multiple submitters ⚠
- p.Gly340Ser Multiple submitters ⚠
- p.Ile109Val Multiple submitters Inborn genetic diseases ⚠
- p.Lys186Glu Multiple submitters ⚠
- p.Pro19Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro21Ser Multiple submitters ⚠
- p.Pro295Leu Multiple submitters ⚠
- p.Pro320Ser Multiple submitters ⚠
- p.Pro330Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro332Ser Multiple submitters ⚠
- p.Pro344Ser Multiple submitters ⚠
- p.Pro348Ala Multiple submitters Inborn genetic diseases ⚠
- p.Pro348Ser Multiple submitters Inborn genetic diseases ⚠
- p.Pro46Leu Multiple submitters Inborn genetic diseases ⚠
- p.Ser315Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ter368Ser Multiple submitters spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
- p.Thr25Ala Multiple submitters Inborn genetic diseases ⚠
- p.Trp336Ter Multiple submitters
- p.Tyr59Cys Multiple submitters Inborn genetic diseases ⚠
- p.Val30Ile Multiple submitters spondylometaphyseal dysplasia-cone-rod dystrophy syndrome ⚠
- c.217+9A>G Single submitter
- c.487-3C>A Single submitter
- c.565+6T>A Single submitter
- c.708+3G>A Single submitter
- c.709-1G>C Single submitter
- p.Ala176Val Single submitter
- p.Ala313Thr Single submitter ⚠
- p.Ala349Val Single submitter Inborn genetic diseases ⚠
- p.Ala3Glu Single submitter ⚠
- p.Ala67Gly Single submitter ⚠
- p.Ala93Ser Single submitter Inborn genetic diseases ⚠
- p.Arg12Ser Single submitter lipodystrophy, congenital generalized, type 5 ⚠
- p.Arg15Ter Single submitter
- p.Arg219Trp Single submitter ⚠
- p.Arg245Ser Single submitter ⚠
- p.Arg283Gln Single submitter ⚠
- p.Arg309Gln Single submitter ⚠
- p.Arg309Pro Single submitter ⚠
- p.Arg326Leu Single submitter ⚠
- p.Arg335Pro Single submitter ⚠
- p.Arg36His Single submitter ⚠
- p.Arg42Gln Single submitter ⚠
- p.Arg61Gly Single submitter ⚠
- p.Arg75Leu Single submitter Inborn genetic diseases ⚠
- p.Arg94Gln Single submitter ⚠
- p.Asn236= Single submitter
- p.Asn350Lys Single submitter ⚠
- p.Asn350Ser Single submitter ⚠
- p.Asp170Asn Single submitter Inborn genetic diseases ⚠
- p.Asp28Gly Single submitter ⚠
- p.Asp367Asn Single submitter ⚠
- p.Cys37Tyr Single submitter Inborn genetic diseases ⚠
- p.Cys5Tyr Single submitter ⚠
- p.Glu17Gly Single submitter Inborn genetic diseases ⚠
- p.Glu269Gly Single submitter Inborn genetic diseases
- p.Glu327Gly Single submitter ⚠
- p.Glu65Gly Single submitter ⚠
- p.Gly199Ala Single submitter Inborn genetic diseases ⚠
- p.Gly20Arg Single submitter ⚠
- p.Gly297Arg Single submitter ⚠
- p.His241Asn Single submitter Inborn genetic diseases ⚠
- p.His354Gln Single submitter ⚠
- p.His354Tyr Single submitter ⚠
- p.Ile200Val Single submitter ⚠
- p.Ile286Thr Single submitter ⚠
- p.Leu102Val Single submitter ⚠
- p.Leu311Pro Single submitter ⚠
- p.Leu351Phe Single submitter ⚠
- p.Lys100Arg Single submitter ⚠
- p.Lys100Asn Single submitter ⚠
- p.Lys259Arg Single submitter ⚠
- p.Lys277Arg Single submitter ⚠
- p.Lys281Arg Single submitter ⚠
- p.Lys341Arg Single submitter ⚠
- p.Lys8Gln Single submitter ⚠
- p.Phe285Tyr Single submitter Inborn genetic diseases ⚠
- p.Phe338fs Single submitter
- p.Pro172fs Single submitter
- p.Pro316Leu Single submitter ⚠
- p.Pro31Leu Single submitter ⚠
- p.Pro44Arg Single submitter ⚠
- p.Pro44Ser Single submitter ⚠
- p.Pro72Thr Single submitter ⚠
- p.Ser260Ter Single submitter
- p.Ser315Asn Single submitter ⚠
- p.Ser315Gly Single submitter ⚠
- p.Ser322Gly Single submitter ⚠
- p.Ser333fs Single submitter
- p.Ser333Pro Single submitter ⚠
- p.Ser347Pro Single submitter ⚠
- p.Ser90Pro Single submitter Inborn genetic diseases ⚠
- p.Thr106Met Single submitter Inborn genetic diseases ⚠
- p.Thr207Ile Single submitter ⚠
- p.Thr25Ile Single submitter Inborn genetic diseases ⚠
- p.Thr342Ala Single submitter ⚠
- p.Trp336Arg Single submitter ⚠
- p.Tyr240Cys Single submitter Inborn genetic diseases ⚠
- p.Tyr359Cys Single submitter Inborn genetic diseases ⚠
- p.Tyr59Ser Single submitter ⚠
- p.Val267Ala Single submitter ⚠
- p.Val267Met Single submitter ⚠
- p.Val30Phe Single submitter ⚠
- p.Val79Ile Single submitter ⚠
- c.897+1G>A No assertion criteria
- p.Ala93Thr No assertion criteria ⚠
- p.Leu41Val No assertion criteria inherited retinal dystrophy ⚠