B3GNT6

Chr 11

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6

Also known as: B3Gn-T6, BGnT-6, beta-1, 3-Gn-T6, beta3Gn-T6

NCBI Gene: 192134 ENSG00000198488 UniProt: O43505 OMIM: 615315

The protein encoded by this gene is a beta-1,3-N-acetylglucosaminyltransferase that adds an N-acetylglucosamine moiety to N-acetylgalactosamine-modified serine or threonine. The encoded enzyme is responsible for creating the core 3 structure of O-glycans, which are important components of mucin-type glycoproteins. [provided by RefSeq, Dec 2016]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtMuscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A13

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.89

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.89LOEUF

pLI 0.000

Z-score -0.93

OE 1.34 (0.84–1.89)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.22Z-score

OE missense 1.04 (0.94–1.16)

247 obs / 237.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.34 (0.84–1.89)

0≤0.351.4

Missense OE?1.04 (0.94–1.16)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 12 / 9.0Missense obs/exp: 247 / 237.6Syn Z: 0.40

Background carrier burden — how many people carry a rare variant somewhere in B3GNT6?

gnomAD v4 · ~730k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 94

673 rare PASS variants

Rare truncating (LoF)

1 in 1,800

82 rare PASS variants

Rare synonymous (reference)

1 in 91

311 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for B3GNT6. 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 110	1 in 2,100
South Asian	~43k	1 in 90	1 in 1,800
Remaining (unassigned)	~30k	1 in 69	1 in 1,600
European (Finnish)	~27k	1 in 480	1 in 2,900
Admixed American	~22k	1 in 69	1 in 1,600
African / African American	~21k	1 in 66	1 in 720
East Asian	~20k	1 in 93	1 in 1,900
Ashkenazi Jewish	~13k	1 in 640	none seen
Middle Eastern	~2,884	1 in 95	≈ 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): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓