COLGALT2

Chr 1

collagen beta(1-O)galactosyltransferase 2

Also known as: C1orf17, ColGalT 2, GLT25D2

NCBI Gene: 23127 ENSG00000198756 UniProt: Q8IYK4 OMIM: 617533

Predicted to enable procollagen galactosyltransferase activity. Predicted to be involved in collagen fibril organization. Predicted to act upstream of or within T cell apoptotic process. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.92

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.92LOEUF

pLI 0.000

Z-score 1.94

OE 0.64 (0.45–0.92)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.81Z-score

OE missense 0.88 (0.80–0.96)

304 obs / 346.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.64 (0.45–0.92)

0≤0.351.4

Missense OE?0.88 (0.80–0.96)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 21 / 33.1Missense obs/exp: 304 / 346.5Syn Z: 0.75

Background carrier burden — how many people carry a rare variant somewhere in COLGALT2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 49

818 rare PASS variants

Rare truncating (LoF)

1 in 1,100

106 rare PASS variants

Rare synonymous (reference)

1 in 130

319 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for COLGALT2. 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 72	1 in 1,100
South Asian	~43k	1 in 61	1 in 560
Remaining (unassigned)	~30k	1 in 49	1 in 2,100
European (Finnish)	~27k	1 in 210	1 in 3,800
Admixed American	~22k	1 in 59	1 in 1,700
African / African American	~21k	1 in 61	1 in 2,200
East Asian	~20k	1 in 82	1 in 970
Ashkenazi Jewish	~13k	1 in 190	1 in 2,200
Middle Eastern	~2,884	1 in 62	≈ 1 in 960

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): 11 of 12 coding exons well covered in gnomAD exomes; exon 2 marginal. Genomes: all 12.? see exons ↓