GCNT3

Chr 15

glucosaminyl (N-acetyl) transferase 3, mucin type

Also known as: C2/4GnT, C24GNT, C2GNT2, C2GNTM, GNTM

NCBI Gene: 9245 ENSG00000140297 UniProt: O95395 OMIM: 606836

This gene encodes a member of the N-acetylglucosaminyltransferase family. The encoded protein is a beta-6-N-acetylglucosamine-transferase that catalyzes the formation of core 2 and core 4 O-glycans on mucin-type glycoproteins.[provided by RefSeq, Apr 2009]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.43

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.43LOEUF

pLI 0.000

Z-score 0.34

OE 0.90 (0.59–1.43)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.65Z-score

OE missense 1.31 (1.19–1.44)

300 obs / 229.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.90 (0.59–1.43)

0≤0.351.4

Missense OE?1.31 (1.19–1.44)

0≤0.61.4

Synonymous OE?1.56

0≤1.21.6

LoF obs/exp: 13 / 14.4Missense obs/exp: 300 / 229.7Syn Z: -4.10

Background carrier burden — how many people carry a rare variant somewhere in GCNT3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 75

763 rare PASS variants

Rare truncating (LoF)

1 in 570

85 rare PASS variants

Rare synonymous (reference)

1 in 120

283 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GCNT3. 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 100	1 in 490
South Asian	~43k	1 in 87	1 in 970
Remaining (unassigned)	~30k	1 in 68	1 in 880
European (Finnish)	~27k	1 in 240	1 in 3,000
Admixed American	~22k	1 in 88	1 in 770
African / African American	~21k	1 in 110	1 in 190
East Asian	~20k	1 in 70	1 in 4,000
Ashkenazi Jewish	~13k	1 in 1,000	1 in 620
Middle Eastern	~2,884	1 in 73	1 in 410

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓