CHST6

carbohydrate sulfotransferase 6, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 16:75472052-75495445

Previous symbols: [ "MCDC1" ]

Links

ENSG00000183196

∙ NCBI:4166 ∙ OMIM:605294 ∙ HGNC:6938 ∙ Uniprot:Q9GZX3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

macular corneal dystrophy (Strong), mode of inheritance: AR
macular corneal dystrophy (Supportive), mode of inheritance: AR
macular corneal dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Macular dystrophy, corneal	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	8684802; 11017086; 11818380; 16207214; 16568029; 17093400; 17896316; 17962390; 19223992; 19365571; 21242781; 21887843; 26604660

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHST6 gene.

Macular_corneal_dystrophy (125 variants)
Inborn_genetic_diseases (67 variants)
not_specified (23 variants)
not_provided (18 variants)
CHST6-related_disorder (9 variants)
Macular_corneal_dystrophy,_type_II (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021615.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	19 clinvar	8 clinvar	33
missense	12 clinvar	12 clinvar	112 clinvar	3 clinvar		139
nonsense	3 clinvar	8 clinvar	1 clinvar			12
start loss		1				1
frameshift	5 clinvar	9 clinvar	2 clinvar			16
splice donor/acceptor (+/-2bp)						0
Total	20	30	121	22	8

Highest pathogenic variant AF is 0.000305979

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST6	protein_coding	protein_coding	ENST00000332272	1	18334

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.45e-9	0.0427	125572	0	38	125610	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.900	334	291	1.15	0.0000263	2462
Missense in Polyphen		136	128.05	1.0621		1129
Synonymous	-0.863	156	143	1.09	0.0000134	921
Loss of Function	-0.624	12	9.88	1.21	5.22e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000463	0.000457
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000327
Finnish	0.00	0.00
European (Non-Finnish)	0.000139	0.000132
Middle Eastern	0.000329	0.000327
South Asian	0.000229	0.000229
Other	0.000675	0.000163

dbNSFP

Source: dbNSFP

Function: 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. Mediates sulfation of keratan in cornea. Keratan sulfate plays a central role in maintaining corneal transparency. Acts on the non-reducing terminal GlcNAc of short and long carbohydrate substrates that have poly-N- acetyllactosamine structures. {ECO:0000269|PubMed:11352640, ECO:0000269|PubMed:12218059}.;
Pathway: Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

pRec: 0.139

Intolerance Scores

loftool: 0.150
rvis_EVS: -0.64
rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

pHI: 0.137
hipred: N
hipred_score: 0.180
ghis: 0.530

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.332

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Chst5
Phenotype: vision/eye phenotype;

Gene ontology

Biological process: carbohydrate metabolic process;N-acetylglucosamine metabolic process;sulfur compound metabolic process;keratan sulfate biosynthetic process
Cellular component: Golgi membrane;Golgi apparatus;trans-Golgi network;integral component of membrane
Molecular function: N-acetylglucosamine 6-O-sulfotransferase activity