A4GNT

Chr 3

alpha-1,4-N-acetylglucosaminyltransferase

Also known as: alpha4GnT

NCBI Gene: 51146 ENSG00000118017 UniProt: Q9UNA3 OMIM: 616709

This gene encodes a protein from the glycosyltransferase 32 family. The enzyme catalyzes the transfer of N-acetylglucosamine (GlcNAc) to core 2 branched O-glycans. It forms a unique glycan, GlcNAcalpha1-->4Galbeta-->R and is largely associated with the Golgi apparatus membrane. [provided by RefSeq, Jul 2008]

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

0.74

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.74LOEUF

pLI 0.165

Z-score 2.14

OE 0.29 (0.13–0.74)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.24Z-score

OE missense 0.95 (0.84–1.08)

179 obs / 188.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.29 (0.13–0.74)

0≤0.351.4

Missense OE?0.95 (0.84–1.08)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 3 / 10.5Missense obs/exp: 179 / 188.1Syn Z: -0.23

Background carrier burden — how many people carry a rare variant somewhere in A4GNT?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 90

414 rare PASS variants

Rare truncating (LoF)

1 in 6,200

38 rare PASS variants

Rare synonymous (reference)

1 in 150

164 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for A4GNT. 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 130	1 in 8,000
South Asian	~43k	1 in 110	1 in 2,900
Remaining (unassigned)	~30k	1 in 110	≈ 1 in 9,900
European (Finnish)	~27k	1 in 840	none seen
Admixed American	~22k	1 in 140	1 in 2,200
African / African American	~21k	1 in 98	1 in 1,100
East Asian	~20k	1 in 260	1 in 4,000
Ashkenazi Jewish	~13k	1 in 380	1 in 2,200
Middle Eastern	~2,884	1 in 90	1 in 320

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): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓