GALNT10

Chr 5

polypeptide N-acetylgalactosaminyltransferase 10

Also known as: GALNACT10, PPGALNACT10, PPGANTASE10

NCBI Gene: 55568ENSG00000164574UniProt: Q86SR1

This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors. The protein encoded by this locus may have increased catalytic activity toward glycosylated peptides compared to activity toward non-glycosylated peptides.[provided by RefSeq, Apr 2010]

0
Active trials
12
Pathogenic / LP
115
ClinVar variants
4
Pubs (1 yr)
1.5
Missense Z
0.64
LOEUF
Clinical Summary— GALNT10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
12 Pathogenic / Likely Pathogenic· 96 VUS of 115 total submissions
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.64LOEUF
pLI 0.000
Z-score 3.22
OE 0.41 (0.27–0.64)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.53Z-score
OE missense 0.78 (0.71–0.86)
292 obs / 375.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.41 (0.27–0.64)
0≤0.351.4
Missense OE0.78 (0.71–0.86)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 14 / 34.3Missense obs/exp: 292 / 375.5Syn Z: 0.11
DNGOF
DN
0.6841th %ile
GOF
0.6345th %ile
LOF
0.3068th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

115 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic12
VUS96
Likely Benign6
Benign1
12
Pathogenic
96
VUS
6
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
12
0
12
Likely Pathogenic
0
0
0
0
0
VUS
0
93
3
0
96
Likely Benign
0
2
3
1
6
Benign
0
0
0
1
1
Total095182115

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

View in ClinVar →

GALNT10 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
GALNT10 promotes the proliferation and metastatic ability of gastric cancer and reduces 5-fluorouracil sensitivity by activating HOXD13.
Xu G et al.·Eur Rev Med Pharmacol Sci
2020
Prioritization of predisposition genes for familial non-medullary thyroid cancer by whole-genome sequencing.
Srivastava A et al.·Eur J Endocrinol
2025
Glycobiology and schizophrenia: a biological hypothesis emerging from genomic research.
Mealer RG et al.·Mol Psychiatry
2020Review
Elevated GALNT10 expression identifies immunosuppressive microenvironment and dismal prognosis of patients with high grade serous ovarian cancer.
Zhang G et al.·Cancer Immunol Immunother
2020Cohort
Targeted plasma proteomics reveals organ damage signatures of AIDS- and noncommunicable disease-related deaths in people with HIV.
Lin H et al.·Nat Commun
2025
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients