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 be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 0.92

Clinical Summary— COLGALT2

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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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

This gene — mechanism propensity

0.6357th %ile

GOF

0.5170th %ile

LOF

0.2775th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.