CHST12

Chr 7

carbohydrate sulfotransferase 12

Also known as: C4S-2, C4ST-2, C4ST2

NCBI Gene: 55501 ENSG00000136213 UniProt: Q9NRB3 OMIM: 610129

The CHST12 protein is a Golgi membrane-localized sulfotransferase that catalyzes sulfate transfer to position 4 of N-acetylgalactosamine residues in chondroitin sulfate and dermatan sulfate, key proteoglycans found in cartilage and extracellular matrices. Biallelic mutations cause autosomal recessive myopathy with glycosaminoglycan storage defects, typically presenting in infancy with muscle weakness and developmental delays. The gene shows low constraint against loss-of-function variants, consistent with recessive inheritance.

OMIM ResearchSummary from RefSeq, UniProt

The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin and desulfated dermatan sulfate. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage, and is distributed on the surfaces of many cells and extracellular matrices. Alternatively spliced transcript variants differing only in their 5' UTRs have been found for this gene. [provided by RefSeq, Aug 2011]

OMIM ResearchGenerating clinical summary…

LOEUF 1.28

Clinical Summary— CHST12

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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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ClinVar Variants

76 VUS of 85 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.28LOEUF

pLI 0.000

Z-score 0.89

OE 0.71 (0.42–1.28)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.15Z-score

OE missense 0.98 (0.89–1.07)

306 obs / 313.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.71 (0.42–1.28)

0≤0.351.4

Missense OE?0.98 (0.89–1.07)

0≤0.61.4

Synonymous OE?1.19

0≤1.21.6

LoF obs/exp: 8 / 11.2Missense obs/exp: 306 / 313.4Syn Z: -1.84

ClinVar Variant Classifications

85 submitted variants in ClinVar

ClinVar

Classification Summary

VUS76

Likely Benign6

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	76	0	76
Likely Benign	4	2	6
Benign	1	0	1
Total	81	2	83

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

View in ClinVar →

36 pathogenic / likely-pathogenic (of 60) ClinVar copy-number / structural variants overlap CHST12 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →