Gene Gene information from NCBI Gene database.
Entrez ID 4166
Gene name Carbohydrate sulfotransferase 6
Gene symbol CHST6
Synonyms (NCBI Gene)
C-GlcNAc6STGST4-betaMCDC1glcNAc6ST-5gn6st-5hCGn6ST
Chromosome 16
Chromosome location 16q23.1
Summary The protein encoded by this gene is an enzyme that catalyzes the transfer of a sulfate group to the GlcNAc residues of keratan. Keratan sulfate helps maintain corneal transparency. Defects in this gene are a cause of macular corneal dystrophy (MCD). [prov
SNPs SNP information provided by dbSNP.
9
SNP ID Visualize variation Clinical significance Consequence
rs28937877 T>C Pathogenic Intron variant, missense variant, coding sequence variant
rs28937878 G>T Pathogenic Intron variant, missense variant, coding sequence variant
rs28937879 A>C Pathogenic Intron variant, missense variant, coding sequence variant
rs72547544 T>C Pathogenic Intron variant, missense variant, coding sequence variant
rs121917822 A>C Pathogenic Intron variant, coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
928
miRTarBase ID miRNA Experiments Reference
MIRT017806 hsa-miR-335-5p Microarray 18185580
MIRT022612 hsa-miR-124-3p Microarray 18668037
MIRT051817 hsa-let-7c-5p CLASH 23622248
MIRT694366 hsa-miR-766-3p HITS-CLIP 23313552
MIRT694365 hsa-miR-4486 HITS-CLIP 23313552
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
24
GO ID Ontology Definition Evidence Reference
GO:0000139 Component Golgi membrane IEA
GO:0000139 Component Golgi membrane TAS
GO:0001517 Function N-acetylglucosamine 6-O-sulfotransferase activity IBA
GO:0001517 Function N-acetylglucosamine 6-O-sulfotransferase activity IDA 11278593, 11352640
GO:0001517 Function N-acetylglucosamine 6-O-sulfotransferase activity IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605294 6938 ENSG00000183196
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9GZX3
Protein name Carbohydrate sulfotransferase 6 (Corneal N-acetylglucosamine-6-O-sulfotransferase) (C-GlcNAc6ST) (hCGn6ST) (EC 2.8.2.21) (Galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 4-beta) (GST4-beta) (N-acetylglucosamine 6-O-sulfotransferase
Protein function Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues of keratan (PubMed:11278593, PubMed:11352640, PubMed:
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00685 Sulfotransfer_1 40 357 Sulfotransferase domain Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in cornea. Mainly expressed in brain. Also expressed in spinal cord and trachea. {ECO:0000269|PubMed:11017086, ECO:0000269|PubMed:11181564, ECO:0000269|PubMed:11352640}.
Sequence
Sequence length 395
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Glycosaminoglycan biosynthesis - keratan sulfate   Keratan sulfate biosynthesis
Defective CHST6 causes MCDC1
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
11
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
CHST6-related disorder Pathogenic rs28937879 RCV004757947
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Macular corneal dystrophy Likely pathogenic; Pathogenic rs2151665554, rs999246452, rs28937877, rs28937878, rs28937879, rs121917822, rs72547544, rs2507252387, rs2080106267, rs746184019, rs2507252174, rs757912368, rs202175444, rs771397083, rs2507253239
View all (5 more)
RCV001731224
RCV001785426
RCV000005375
RCV000005376
RCV000005379
View all (15 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Macular corneal dystrophy, type II Pathogenic rs28937879 RCV000005380
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
AUTISM SPECTRUM DISORDER CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DIVERTICULAR DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Age related macular degeneration Age-related macular degeneration HPO_DG
★☆☆☆☆
Found in Text Mining only
Amyloidosis Amyloidosis BEFREE 21242781
★☆☆☆☆
Found in Text Mining only
Amyloidosis Amyloidosis Pubtator 21242781 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Renal Cell Renal cell carcinoma Pubtator 33836688, 40149981 Associate
★☆☆☆☆
Found in Text Mining only
Corneal Diseases Corneal disease Pubtator 14735064, 16568029 Associate
★☆☆☆☆
Found in Text Mining only
Corneal Dystrophies Hereditary Corneal dystrophy Pubtator 11139648, 14735064, 16568029, 19204788, 19223992, 19365571, 21242781, 24311932, 25081284, 26604660, 27439461, 27829782, 31669782, 34301210, 34645431
View all (3 more)
Associate
★☆☆☆☆
Found in Text Mining only
Corneal dystrophy Corneal Dystrophy BEFREE 17896316, 21887843, 24801599
★☆☆☆☆
Found in Text Mining only
Corneal dystrophy Corneal Dystrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Corneal dystrophy Avellino type Corneal dystrophy Pubtator 21887843 Associate
★☆☆☆☆
Found in Text Mining only
Corneal hypoesthesia Corneal Hypoesthesia HPO_DG
★☆☆☆☆
Found in Text Mining only