CHST6

carbohydrate sulfotransferase 6, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 16:75472051-75495445

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

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 (240 variants)
• Inborn genetic diseases (27 variants)
• not provided (10 variants)
• not specified (5 variants)
• Macular corneal dystrophy, type II (1 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.

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			6	8	8	22
missense	6	1	66		2	75
nonsense	3	2	2			7
start loss	1					1
frameshift	2		1			3
inframe indel	1					1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			102	16	37	155
Total	13	3	177	24	47

Highest pathogenic variant AF is 0.000210

Variants in CHST6

This is a list of pathogenic ClinVar variants found in the CHST6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-75473176-G-A		Macular corneal dystrophy	Benign (Jan 13, 2018)
16-75473189-C-G		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473196-C-T		Macular corneal dystrophy	Benign (Jan 12, 2018)
16-75473200-G-A		Macular corneal dystrophy	Benign (Jan 12, 2018)
16-75473330-A-G		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)
16-75473355-T-A		Macular corneal dystrophy	Benign (Jan 12, 2018)
16-75473433-G-A		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473444-G-A		Macular corneal dystrophy	Likely benign (Jan 12, 2018)
16-75473451-A-T		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473454-A-C		Macular corneal dystrophy	Benign (Jan 13, 2018)
16-75473458-C-T		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473459-G-C		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)
16-75473491-C-T		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473492-G-A		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)
16-75473630-C-T		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473660-G-A		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473671-A-G		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75473699-G-A		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)
16-75473761-C-T		Macular corneal dystrophy	Likely benign (Jan 12, 2018)
16-75473892-C-A		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)
16-75474036-G-A		Macular corneal dystrophy	Benign (Jan 13, 2018)
16-75474052-G-A		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75474055-A-G		Macular corneal dystrophy	Uncertain significance (Jan 13, 2018)
16-75474067-C-G		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)
16-75474068-G-A		Macular corneal dystrophy	Uncertain significance (Jan 12, 2018)

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