CHST6
Basic information
Region (hg38): 16:75472052-75495445
Previous symbols: [ "MCDC1" ]
Links
Phenotypes
GenCC
Source:
- 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:
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
- Macular corneal dystrophy (16 variants)
- not provided (1 variants)
- Macular corneal dystrophy, type II (1 variants)
- CHST6-related disorder (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 | 12 | 26 | ||||
missense | 10 | 91 | 111 | |||
nonsense | 11 | |||||
start loss | 1 | |||||
frameshift | 13 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 102 | 16 | 37 | 155 | ||
Total | 16 | 26 | 201 | 28 | 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:
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:
- 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