GALNT5

Chr 2

polypeptide N-acetylgalactosaminyltransferase 5

Also known as: GALNAC-T5, GALNACT5

NCBI Gene: 11227 ENSG00000136542 UniProt: Q7Z7M9

The protein encoded by this gene is a membrane-bound polypeptide N-acetylgalactosaminyltransferase that is found in the Golgi. The encoded protein catalyzes the first step in the mucin-type O-glycosylation of Golgi proteins, transfering an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. [provided by RefSeq, Aug 2016]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.98

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.98LOEUF

pLI 0.000

Z-score 1.64

OE 0.71 (0.52–0.98)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.48Z-score

OE missense 0.94 (0.87–1.01)

455 obs / 484.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.71 (0.52–0.98)

0≤0.351.4

Missense OE?0.94 (0.87–1.01)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 26 / 36.8Missense obs/exp: 455 / 484.6Syn Z: -0.38

Background carrier burden — how many people carry a rare variant somewhere in GALNT5?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 50

1,225 rare PASS variants

Rare truncating (LoF)

1 in 490

186 rare PASS variants

Rare synonymous (reference)

1 in 130

436 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GALNT5. 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 61	1 in 520
South Asian	~43k	1 in 56	1 in 840
Remaining (unassigned)	~30k	1 in 42	1 in 270
European (Finnish)	~27k	1 in 140	1 in 480
Admixed American	~22k	1 in 46	1 in 430
African / African American	~21k	1 in 37	1 in 420
East Asian	~20k	1 in 51	1 in 510
Ashkenazi Jewish	~13k	1 in 510	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 50	1 in 220

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): 7 of 10 coding exons well covered in gnomAD exomes; exons 5, 6, 8 marginal. Genomes: all 10.? see exons ↓