CHST9

carbohydrate sulfotransferase 9, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 18:26906481-27185308

Links

ENSG00000154080NCBI:83539OMIM:610191HGNC:19898Uniprot:Q7L1S5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHST9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
1
clinvar
2
missense
25
clinvar
25
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 25 1 1

Variants in CHST9

This is a list of pathogenic ClinVar variants found in the CHST9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
18-26916359-C-T not specified Uncertain significance (Jan 08, 2024)3144776
18-26916412-G-C Benign (Feb 25, 2018)788912
18-26916443-A-T not specified Uncertain significance (Oct 12, 2021)2223701
18-26916447-G-C not specified Uncertain significance (Oct 05, 2023)3144775
18-26916515-G-A not specified Uncertain significance (Dec 17, 2023)3144774
18-26916527-T-G not specified Uncertain significance (May 24, 2024)3267253
18-26916531-T-A not specified Uncertain significance (Jan 23, 2024)3144773
18-26916650-C-T not specified Uncertain significance (Oct 26, 2022)2357114
18-26916675-C-T not specified Uncertain significance (Jun 17, 2024)3267255
18-26916702-G-T not specified Uncertain significance (Mar 08, 2024)3144782
18-26916743-A-T not specified Uncertain significance (Jul 12, 2022)2300618
18-26916799-T-A not specified Uncertain significance (May 03, 2023)2543258
18-26916807-C-T not specified Uncertain significance (Nov 23, 2022)2224227
18-26916982-T-C Likely benign (Apr 01, 2022)2648627
18-26916989-T-C not specified Uncertain significance (May 08, 2023)2524813
18-26917017-C-A not specified Uncertain significance (Aug 20, 2023)2609011
18-26917082-T-A not specified Uncertain significance (Jun 12, 2023)2559761
18-26917099-T-A not specified Uncertain significance (Dec 21, 2023)3144781
18-26917100-T-C not specified Uncertain significance (Jan 08, 2024)3144780
18-26917140-A-G not specified Uncertain significance (May 17, 2023)2551751
18-26917144-C-T not specified Uncertain significance (Aug 13, 2021)2370598
18-26917257-T-G not specified Uncertain significance (May 27, 2022)2284047
18-26917278-T-C not specified Uncertain significance (Jun 07, 2023)2558508
18-26917319-C-T not specified Uncertain significance (Apr 23, 2024)3267256
18-27024128-C-T not specified Uncertain significance (Sep 22, 2022)2344688

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CHST9protein_codingprotein_codingENST00000284224 5269687
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.95e-90.45012461211711247840.000689
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.03442252241.010.00001152942
Missense in Polyphen92100.230.917911296
Synonymous1.496481.00.7900.00000416782
Loss of Function0.9631519.60.7650.00000110261

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004110.00411
Ashkenazi Jewish0.0002000.000199
East Asian0.002850.00279
Finnish0.0004650.000464
European (Non-Finnish)0.0002950.000291
Middle Eastern0.002850.00279
South Asian0.0002630.000261
Other0.000.00

dbNSFP

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.;
Pathway
Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

pRec
0.0897

Intolerance Scores

loftool
0.749
rvis_EVS
-0.05
rvis_percentile_EVS
50.01

Haploinsufficiency Scores

pHI
0.299
hipred
N
hipred_score
0.180
ghis
0.452

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.259

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Chst9
Phenotype

Gene ontology

Biological process
sulfur compound metabolic process;carbohydrate biosynthetic process;proteoglycan biosynthetic process;glycosaminoglycan metabolic process;chondroitin sulfate biosynthetic process;hormone biosynthetic process
Cellular component
Golgi membrane;extracellular region;integral component of membrane
Molecular function
N-acetylgalactosamine 4-O-sulfotransferase activity;chondroitin 4-sulfotransferase activity