GALNT13

Chr 2

polypeptide N-acetylgalactosaminyltransferase 13

NCBI Gene: 114805 ENSG00000144278 UniProt: Q8IUC8 OMIM: 608369

The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.28

LOEUF· LoF intol.

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.28LOEUF

pLI 0.991

Z-score 4.30

OE 0.11 (0.05–0.28)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.27Z-score

OE missense 0.79 (0.71–0.88)

236 obs / 297.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.11 (0.05–0.28)

0≤0.351.4

Missense OE?0.79 (0.71–0.88)

0≤0.61.4

Synonymous OE?0.91

0≤1.21.6

LoF obs/exp: 3 / 27.3Missense obs/exp: 236 / 297.6Syn Z: 0.70

Background carrier burden — how many people carry a rare variant somewhere in GALNT13?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

700 rare PASS variants

Rare truncating (LoF)

1 in 1,100

81 rare PASS variants

Rare synonymous (reference)

1 in 130

260 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GALNT13. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 170	1 in 900
South Asian	~43k	1 in 120	1 in 980
Remaining (unassigned)	~30k	1 in 88	1 in 2,500
European (Finnish)	~27k	1 in 270	1 in 2,400
Admixed American	~22k	1 in 98	1 in 2,800
African / African American	~21k	1 in 180	≈ 1 in 5,600
East Asian	~20k	1 in 120	≈ 1 in 4,900
Ashkenazi Jewish	~13k	1 in 1,400	1 in 1,600
Middle Eastern	~2,884	1 in 90	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 9 of 11 coding exons well covered in gnomAD exomes; exons 8, 11 marginal. Genomes: all 11.? see exons ↓