CHST9

Chr 18

carbohydrate sulfotransferase 9

Also known as: GALNAC4ST-2, GalNAc4ST2

NCBI Gene: 83539ENSG00000154080UniProt: Q7L1S5

The protein is a Golgi-localized sulfotransferase that catalyzes the transfer of sulfate to N-acetylgalactosamine residues in N-glycans and O-glycans, and is required for biosynthesis of the glycoprotein hormones lutropin and thyrotropin. Mutations cause autosomal recessive hypogonadotropic hypogonadism with hypothyroidism, typically presenting in infancy with growth delays and developmental issues. The gene is not highly constrained against loss-of-function variants.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
2
Pubs (1 yr)
37
P/LP submissions
0%
P/LP missense
1.18
LOEUF
DN
Mechanism· predicted
Clinical Summary— CHST9
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
35 unique Pathogenic / Likely Pathogenic· 67 VUS of 115 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.18LOEUF
pLI 0.000
Z-score 0.96
OE 0.77 (0.51–1.18)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.03Z-score
OE missense 1.01 (0.90–1.12)
225 obs / 223.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.77 (0.51–1.18)
0≤0.351.4
Missense OE1.01 (0.90–1.12)
0≤0.61.4
Synonymous OE0.79
0≤1.21.6
LoF obs/exp: 15 / 19.6Missense obs/exp: 225 / 223.6Syn Z: 1.49
DN
0.6938th %ile
GOF
0.6052th %ile
LOF
0.2873th %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.

ClinVar Variant Classifications

115 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic34
Likely Pathogenic1
VUS67
Likely Benign5
Benign1
34
Pathogenic
1
Likely Pathogenic
67
VUS
5
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
34
0
34
Likely Pathogenic
0
0
1
0
1
VUS
0
58
9
0
67
Likely Benign
0
2
1
2
5
Benign
0
0
0
1
1
Total060453108

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

View in ClinVar →

Protein Context — Lollipop Plot

CHST9 · 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.

Search ClinicalTrials.gov →
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
CHST9 rs1436904 genetic variant contributes to prognosis of triple-negative breast cancer.
Yuan J et al.·Sci Rep
2017Clinical trial
Large-scale genome-wide analyses with proteomics integration reveal novel loci and biological insights into frailty.
Mak JKL et al.·Nat Aging
2025Meta-analysis
A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population.
Chen J et al.·Sci Rep
2019Clinical trial
DNA methylation mediates the genetic variants on ticagrelor major metabolite elimination and platelet function recovery after ticagrelor discontinuation.
Xu G et al.·Epigenomics
2022Clinical trial
Identification of EGFR expression status association with metastatic lymph node density (ND) by expression microarray analysis of advanced gastric cancer.
Ema A et al.·Cancer Med
2015
Top 5 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