C1GALT1

Chr 7

core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1

Also known as: C1GALT, T-synthase

NCBI Gene: 56913ENSG00000106392UniProt: Q9NS00

The protein encoded by this gene generates the common core 1 O-glycan structure, Gal-beta-1-3GalNAc-R, by the transfer of Gal from UDP-Gal to GalNAc-alpha-1-R. Core 1 is a precursor for many extended mucin-type O-glycans on cell surface and secreted glycoproteins. Studies in mice suggest that this gene plays a key role in thrombopoiesis and kidney homeostasis.[provided by RefSeq, Sep 2010]

95
ClinVar variants
29
Pathogenic / LP
0.76
pLI score
0
Active trials
Clinical Summary— C1GALT1
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.76) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
29 Pathogenic / Likely Pathogenic· 52 VUS of 95 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.47LOEUF
pLI 0.763
Z-score 2.90
OE 0.15 (0.06–0.47)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.12Z-score
OE missense 0.98 (0.86–1.10)
184 obs / 188.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.15 (0.06–0.47)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.98 (0.86–1.10)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.18
0≤1.21.6
LoF obs/exp: 2 / 13.5Missense obs/exp: 184 / 188.6Syn Z: -1.16

ClinVar Variant Classifications

95 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic29
VUS52
Likely Benign12
Benign2
29
Pathogenic
52
VUS
12
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
29
0
29
Likely Pathogenic
0
0
0
0
0
VUS
0
44
8
0
52
Likely Benign
0
2
9
1
12
Benign
0
1
1
0
2
Total04747195

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

C1GALT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Bioinformatic Analysis of C1GALT1 in Cancer: Insights Into Prognosis, Metastasis and Therapeutic Potential.
Kalemoglu E et al.·Cancer Rep (Hoboken)
2025
C1GALT1 high expression enhances the progression of glioblastoma through the EGFR-AKT/ERK cascade.
Su Y et al.·Cell Signal
2025
C1GALT1 expression predicts poor survival in osteosarcoma and is crucial for ABCC1 transporter-mediated doxorubicin resistance.
Liu CW et al.·J Pathol
2025
In-depth quantitative proteomics analysis revealed C1GALT1 depletion in ECC-1 cells mimics an aggressive endometrial cancer phenotype observed in cancer patients with low C1GALT1 expression.
Montero-Calle A et al.·Cell Oncol (Dordr)
2023Cohort
Sialyl-T Antigen: A Novel Red Blood Cell Determinant for Plasmodium falciparum Invasion.
Mikdar M et al.·Am J Hematol
2025
Pathogenic glycosyltransferase genes and potential therapeutic drugs in pressure overload-induced heart failure.
Wu J et al.·ESC Heart Fail
2025
Genetic variant of C1GalT1 contributes to the susceptibility to IgA nephropathy.
Pirulli D et al.·J Nephrol
2009
Cytokines alter IgA1 O-glycosylation by dysregulating C1GalT1 and ST6GalNAc-II enzymes.
Suzuki H et al.·J Biol Chem
2014
Association analysis of DNA methyltransferases in IgA nephropathy.
Xia M et al.·Int Immunopharmacol
2020
Germline C1GALT1C1 mutation causes a multisystem chaperonopathy.
Erger F et al.·Proc Natl Acad Sci U S A
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools