CSGALNACT2

Chr 10

chondroitin sulfate N-acetylgalactosaminyltransferase 2

Also known as: CHGN2, ChGn-2, GALNACT-2, GALNACT2, PRO0082, beta4GalNAcT

NCBI Gene: 55454ENSG00000169826UniProt: Q8N6G5

The encoded protein transfers N-acetylgalactosamine to glucuronic acid during chondroitin sulfate synthesis, functioning in both initial core tetrasaccharide modification and chondroitin chain elongation. Mutations cause autosomal recessive spondyloepimetaphyseal dysplasia with joint laxity, characterized by skeletal abnormalities and connective tissue involvement. The gene shows moderate constraint against loss-of-function variants, supporting its essential role in skeletal development.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
4
Pubs (1 yr)
13
P/LP submissions
0%
P/LP missense
0.48
LOEUF
—
Mechanism
Clinical Summary— CSGALNACT2
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.24) despite low pLI — interpret in context.
📋
ClinVar Variants
13 unique Pathogenic / Likely Pathogenic· 77 VUS of 107 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.48LOEUF
pLI 0.238
Z-score 3.51
OE 0.24 (0.13–0.48)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.12Z-score
OE missense 0.82 (0.73–0.91)
243 obs / 297.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.24 (0.13–0.48)
0≤0.351.4
Missense OE0.82 (0.73–0.91)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 6 / 24.9Missense obs/exp: 243 / 297.3Syn Z: 0.12

ClinVar Variant Classifications

107 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
Likely Pathogenic2
VUS77
Likely Benign4
Benign1
11
Pathogenic
2
Likely Pathogenic
77
VUS
4
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
2
0
2
VUS
0
74
3
0
77
Likely Benign
0
4
0
0
4
Benign
0
0
1
0
1
Total07817095

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CSGALNACT2 · 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

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients