C1GALT1C1 — 57 ClinVar variants
All ClinVar germline C1GALT1C1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 37 flagged for review →
6 Pathogenic · 2 Likely pathogenic · 3 Benign · 1 Benign/Likely benign · 12 Likely benign · 33 Uncertain significance
Full C1GALT1C1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 37
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 20
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
C1GALT1C1 p.Asn202Lys
Uncertain significance
Multiple submitters
Tn polyagglutination syndrome
-
C1GALT1C1 p.Gly314Arg
Uncertain significance
Multiple submitters
Tn polyagglutination syndrome
- C1GALT1C1 p.Ala306Thr Uncertain significance Single submitter
-
C1GALT1C1 p.Arg35Ser
Uncertain significance
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Asn317Ser Uncertain significance Single submitter
- C1GALT1C1 p.Asp117Glu Uncertain significance Single submitter
- C1GALT1C1 p.Gln222Arg Uncertain significance Single submitter
- C1GALT1C1 p.Gly252Glu Uncertain significance Single submitter
- C1GALT1C1 p.His171Gln Uncertain significance Single submitter
- C1GALT1C1 p.Ile150Val Uncertain significance Single submitter
- C1GALT1C1 p.Ile255Val Uncertain significance Single submitter
-
C1GALT1C1 p.Leu158Phe
Uncertain significance
Single submitter
hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature
- C1GALT1C1 p.Leu307Phe Uncertain significance Single submitter
-
C1GALT1C1 p.Lys106Arg
Uncertain significance
Single submitter
Tn polyagglutination syndrome
-
C1GALT1C1 p.Lys221Arg
Uncertain significance
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Lys65Glu Uncertain significance Single submitter
-
C1GALT1C1 p.Met113Thr
Uncertain significance
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Thr172Ser Uncertain significance Single submitter
-
C1GALT1C1 p.Val276Ala
Uncertain significance
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Val276Ile Uncertain significance Single submitter
Predictors split 17
The independent predictors disagree with each other — read with care.
-
C1GALT1C1 p.Ala143Val
Benign
Multiple submitters
Tn polyagglutination syndrome
-
C1GALT1C1 p.Arg60Cys
Uncertain significance
Multiple submitters
Tn polyagglutination syndrome
-
C1GALT1C1 p.Ser101Asn
Benign
Multiple submitters
Tn polyagglutination syndrome
-
C1GALT1C1 p.Ala20Asp
Likely pathogenic
Single submitter
Abnormal protein O-linked glycosylation
-
C1GALT1C1 p.Arg144Cys
Uncertain significance
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Arg29Met Uncertain significance Single submitter
- C1GALT1C1 p.Arg60His Uncertain significance Single submitter
- C1GALT1C1 p.Asp131Asn Uncertain significance Single submitter
-
C1GALT1C1 p.Asp51Gly
Uncertain significance
Single submitter
Tn polyagglutination syndrome
-
C1GALT1C1 p.Gln222His
Likely benign
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Glu257Gln Uncertain significance Single submitter
-
C1GALT1C1 p.Pro47Ser
Uncertain significance
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Ser199Arg Uncertain significance Single submitter
- C1GALT1C1 p.Ser250Phe Uncertain significance Single submitter
- C1GALT1C1 p.Thr146Ala Uncertain significance Single submitter
-
C1GALT1C1 p.Thr147Met
Likely benign
Single submitter
Tn polyagglutination syndrome
- C1GALT1C1 p.Val75Leu Uncertain significance Single submitter
All C1GALT1C1 variants
Pathogenic 6
- p.Arg68Ter Single submitter Tn polyagglutination syndrome
- p.Thr89Ile Single submitter atypical hemolytic-uremic syndrome
- p.Glu152Lys No assertion criteria Tn polyagglutination syndrome
- p.Met1Ile No assertion criteria Tn polyagglutination syndrome
- p.Ser193Pro No assertion criteria Tn polyagglutination syndrome
- p.Tyr180Ter No assertion criteria Tn polyagglutination syndrome
Likely pathogenic 2
- p.Ala20Asp Single submitter Abnormal protein O-linked glycosylation ⚠
- p.Gly185Arg Single submitter hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature
Benign 3
- p.Ala143Val Multiple submitters Tn polyagglutination syndrome ⚠
- p.Ser101Asn Multiple submitters Tn polyagglutination syndrome ⚠
- p.Met24Val Single submitter Tn polyagglutination syndrome
Benign/Likely benign 1
- p.Asp131Glu Multiple submitters hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature
Likely benign 12
- p.Ala298= Single submitter Tn polyagglutination syndrome
- p.Arg29= Single submitter Tn polyagglutination syndrome
- p.Gln222His Single submitter Tn polyagglutination syndrome ⚠
- p.Gln45= Single submitter Tn polyagglutination syndrome
- p.Gly212= Single submitter Tn polyagglutination syndrome
- p.Ile72= Single submitter Tn polyagglutination syndrome
- p.Leu154= Single submitter Tn polyagglutination syndrome
- p.Ser66= Single submitter Tn polyagglutination syndrome
- p.Thr147= Single submitter Tn polyagglutination syndrome
- p.Thr147Met Single submitter Tn polyagglutination syndrome ⚠
- p.Thr248= Single submitter Tn polyagglutination syndrome
- p.Tyr70= Single submitter Tn polyagglutination syndrome
Uncertain significance 33
- p.Arg60Cys Multiple submitters Tn polyagglutination syndrome ⚠
- p.Asn202Lys Multiple submitters Tn polyagglutination syndrome ⚠
- p.Gly314Arg Multiple submitters Tn polyagglutination syndrome ⚠
- p.Ala306Thr Single submitter ⚠
- p.Arg144Cys Single submitter Tn polyagglutination syndrome ⚠
- p.Arg29Met Single submitter ⚠
- p.Arg35Ser Single submitter Tn polyagglutination syndrome ⚠
- p.Arg60His Single submitter ⚠
- p.Asn317Ser Single submitter ⚠
- p.Asp117Glu Single submitter ⚠
- p.Asp131Asn Single submitter ⚠
- p.Asp51Gly Single submitter Tn polyagglutination syndrome ⚠
- p.Gln222Arg Single submitter ⚠
- p.Glu257Gln Single submitter ⚠
- p.Gly252Glu Single submitter ⚠
- p.His171Gln Single submitter ⚠
- p.Ile150Val Single submitter ⚠
- p.Ile255Val Single submitter ⚠
- p.Leu158Phe Single submitter hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature ⚠
- p.Leu307Phe Single submitter ⚠
- p.Lys106Arg Single submitter Tn polyagglutination syndrome ⚠
- p.Lys221Arg Single submitter Tn polyagglutination syndrome ⚠
- p.Lys65Glu Single submitter ⚠
- p.Lys65Ter Single submitter hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature
- p.Met113Thr Single submitter Tn polyagglutination syndrome ⚠
- p.Pro47Ser Single submitter Tn polyagglutination syndrome ⚠
- p.Ser199Arg Single submitter ⚠
- p.Ser250Phe Single submitter ⚠
- p.Thr146Ala Single submitter ⚠
- p.Thr172Ser Single submitter ⚠
- p.Val276Ala Single submitter Tn polyagglutination syndrome ⚠
- p.Val276Ile Single submitter ⚠
- p.Val75Leu Single submitter ⚠