B3GALNT1

Chr 3

beta-1,3-N-acetylgalactosaminyltransferase 1 (Globoside blood group)

NCBI Gene: 8706 ENSG00000169255 UniProt: O75752 OMIM: 603094

Transfers N-acetylgalactosamine onto globotriaosylceramide (PubMed:10993897). Plays a critical role in preimplantation stage embryonic development (By similarity)

OMIM Research

Transfers N-acetylgalactosamine onto globotriaosylceramide (PubMed:10993897). Plays a critical role in preimplantation stage embryonic development (By similarity)

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

[Blood group, globoside system]MIM #615021

[Blood group, P1PK system, P(k) phenotype]MIM #111400

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.00

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.00LOEUF

pLI 0.002

Z-score 1.58

OE 0.51 (0.28–1.00)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.75Z-score

OE missense 0.84 (0.73–0.96)

145 obs / 172.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.51 (0.28–1.00)

0≤0.351.4

Missense OE?0.84 (0.73–0.96)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 6 / 11.9Missense obs/exp: 145 / 172.7Syn Z: -0.25

Background carrier burden — how many people carry a rare variant somewhere in B3GALNT1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 320

377 rare PASS variants

Rare truncating (LoF)

1 in 1,600

57 rare PASS variants

Rare synonymous (reference)

1 in 520

148 rare PASS variants

Rare missense and truncating variants are carried at similar rates in B3GALNT1; this gene does not show strong loss-of-function constraint by this measure. 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 420	1 in 2,500
South Asian	~43k	1 in 260	1 in 1,300
Remaining (unassigned)	~30k	1 in 360	1 in 1,200
European (Finnish)	~27k	1 in 2,700	1 in 5,300
Admixed American	~22k	1 in 230	1 in 2,800
African / African American	~21k	1 in 200	1 in 3,100
East Asian	~20k	1 in 270	1 in 3,300
Ashkenazi Jewish	~13k	≈ 1 in 4,200	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 480	≈ 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 ↓