CHST9

protein-coding

carbohydrate sulfotransferase 9, the group of Sulfotransferases, membrane bound

Gene summary

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 non-reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans. Sulfate groups on carbohydrates confer highly specific functions to glycoproteins, glycolipids, and proteoglycans, and are critical for cell-cell interaction, signal transduction, and embryonic development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Aug 2011]

MANE transcript

NM_031422.6

Inheritance

—

ClinVar variants

U:61B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr18:26,906,481-27,185,308

External References & Databases

Ensembl (ENSG00000154080)

Transcript & Mutation Effects

hg38 • Region Span ~278.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHST9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031422.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense			59 clinvar	2 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	4	1	66

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031422.6	RefSeq	NP_113610.2	5	MANE Select
ENST00000618847.5	Ensembl	ENSP00000480991.1	5	MANE Select
NM_001256316.2	RefSeq	NP_001243245.1	4	Standard
NM_001398493.1	RefSeq	NP_001385422.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metapathway biotransformation Phase I and II
Metabolism of carbohydrates
Chondroitin sulfate biosynthesis
Chondroitin sulfate/dermatan sulfate metabolism
Glycosaminoglycan metabolism

Biological Process

sulfur compound metabolic process
carbohydrate biosynthetic process
proteoglycan biosynthetic process
glycosaminoglycan metabolic process
chondroitin sulfate biosynthetic process

Molecular Function

N-acetylgalactosamine 4-O-sulfotransferase activity
chondroitin 4-sulfotransferase activity

Cellular Component

Golgi membrane
extracellular region
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000284224
Coding exons: 5
Length: 269687
Individuals with no LoFs: 124612
Homozygous LoFs: 1
Heterozygous LoFs: 171
Defined: 124784
p: 0.000689

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0344	225	224	1.01	0.0000115	2942
Missense (PolyPhen)		92	100.23	0.91791		1296
Synonymous	1.49	64	81.0	0.790	0.00000416	782
Loss of Function	0.963	15	19.6	0.765	0.00000110	261

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0038	0.0038	notable
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0029	0.0028	notable
Finnish	0.00047	0.00046	rare
European (Non-Finnish)	0.00029	0.00029	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the transfer of sulfate to position 4 of non- reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans. Participates in biosynthesis of glycoprotein hormones lutropin and thyrotropin, by mediating sulfation of their carbohydrate structures. Has a higher activity toward carbonic anhydrase VI than toward lutropin. Only active against terminal GalNAcbeta1,GalNAcbeta. Isoform 2, but not isoform 1, is active toward chondroitin.;

Recessive Scores

pRec: 0.0897

Intolerance Scores

LoFtool: 0.749
RVIS EVS: -0.05
RVIS percentile EVS: 50.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.259

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium