CHST2

Chr 3

carbohydrate sulfotransferase 2

Also known as: C6ST, GST-2, GST2, Gn6ST-1, HEL-S-75, glcNAc6ST-1

NCBI Gene: 9435 ENSG00000175040 UniProt: Q9Y4C5 OMIM: 603798

This locus encodes a sulfotransferase protein. The encoded enzyme catalyzes the sulfation of a nonreducing N-acetylglucosamine residue, and may play a role in biosynthesis of 6-sulfosialyl Lewis X antigen. [provided by RefSeq, Aug 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.81

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.81LOEUF

pLI 0.018

Z-score 2.05

OE 0.39 (0.20–0.81)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

2.14Z-score

OE missense 0.66 (0.59–0.74)

209 obs / 316.2 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.39 (0.20–0.81)

0≤0.351.4

Missense OE?0.66 (0.59–0.74)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 5 / 13.0Missense obs/exp: 209 / 316.2Syn Z: 0.53

Background carrier burden — how many people carry a rare variant somewhere in CHST2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 100

773 rare PASS variants

Rare truncating (LoF)

1 in 4,400

83 rare PASS variants

Rare synonymous (reference)

1 in 120

416 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CHST2. 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 140	1 in 5,200
South Asian	~43k	1 in 74	1 in 2,900
Remaining (unassigned)	~30k	1 in 93	1 in 3,600
European (Finnish)	~27k	1 in 240	1 in 3,100
Admixed American	~22k	1 in 100	1 in 2,400
African / African American	~21k	1 in 92	≈ 1 in 5,600
East Asian	~20k	1 in 99	1 in 3,200
Ashkenazi Jewish	~13k	1 in 220	≈ 1 in 4,100
Middle Eastern	~2,884	1 in 120	none seen

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): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓