CSGALNACT1

Chr 8AR

chondroitin sulfate N-acetylgalactosaminyltransferase 1

Also known as: CSGalNAcT-1, ChGn, ChGn-1, SDJLABA, beta4GalNAcT

This enzyme transfers N-acetylgalactosamine to glucuronic acid residues during chondroitin sulfate biosynthesis, which is essential for cartilage formation and endochondral ossification. Autosomal recessive mutations cause skeletal dysplasia with joint laxity and advanced bone age, primarily affecting the musculoskeletal system. The gene shows low constraint against loss-of-function variants (LOEUF 1.338), consistent with the recessive inheritance pattern where heterozygous carriers are typically unaffected.

OMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 1.341 OMIM phenotype
Clinical SummaryCSGALNACT1
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Gene-Disease Validity (ClinGen)
skeletal dysplasia, mild, with joint laxity and advanced bone age · ARModerate

Moderate evidence — consider for supplementary testing

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

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.34LOEUF
pLI 0.000
Z-score 0.31
OE 0.93 (0.661.34)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-2.63Z-score
OE missense 1.43 (1.321.55)
425 obs / 297.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.93 (0.661.34)
00.351.4
Missense OE1.43 (1.321.55)
00.61.4
Synonymous OE1.49
01.21.6
LoF obs/exp: 21 / 22.6Missense obs/exp: 425 / 297.4Syn Z: -4.14

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CSGALNACT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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