CHST11
carbohydrate sulfotransferase 11, the group of Sulfotransferases, membrane bound|MicroRNA protein coding host genes
Basic information
Region (hg38): 12:104455294-104762014
Links
Phenotypes
GenCC
Source:
- osteochondrodysplasia, brachydactyly, and overlapping malformed digits (Limited), mode of inheritance: AR
- osteochondrodysplasia, brachydactyly, and overlapping malformed digits (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Osteochondrodysplasia, brachydactyly, and overlapping malformed digits | 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 | Musculoskeletal | 26436107; 29514872 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST11 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 | |||||
| missense | 15 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 15 | 5 | 0 |
Variants in CHST11
This is a list of pathogenic ClinVar variants found in the CHST11 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-104457405-C-A | CHST11-related disorder | Likely benign (Feb 19, 2024) | ||
| 12-104457415-A-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 12-104457433-G-A | not specified | Uncertain significance (Oct 25, 2023) | ||
| 12-104457440-G-A | not specified | Uncertain significance (Jun 13, 2024) | ||
| 12-104457506-A-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-104601912-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 12-104601961-C-T | CHST11-related disorder | Likely benign (Feb 18, 2019) | ||
| 12-104756949-C-T | not specified | Likely benign (Nov 02, 2023) | ||
| 12-104756989-G-A | not specified | Uncertain significance (Jun 23, 2023) | ||
| 12-104757034-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 12-104757039-C-T | not specified | Uncertain significance (May 08, 2024) | ||
| 12-104757040-G-A | CHST11-related disorder | Likely benign (Apr 10, 2023) | ||
| 12-104757045-G-A | not specified | Uncertain significance (Apr 13, 2022) | ||
| 12-104757221-CAACCTGAAGACCCTG-C | Brachydactyly;Synpolydactyly type 1;clino-symphalangism;overriding digits;Chondrodysplasia • Osteochondrodysplasia, brachydactyly, and overlapping malformed digits | Conflicting classifications of pathogenicity (Jan 10, 2019) | ||
| 12-104757230-G-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 12-104757262-A-G | not specified | Uncertain significance (Jan 04, 2022) | ||
| 12-104757268-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 12-104757312-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 12-104757399-C-T | not specified | Uncertain significance (Aug 31, 2022) | ||
| 12-104757403-A-G | not specified | Uncertain significance (Jan 24, 2024) | ||
| 12-104757414-G-C | CHST11-related disorder | Likely benign (Aug 01, 2023) | ||
| 12-104757441-G-A | not specified | Uncertain significance (Feb 17, 2024) | ||
| 12-104757456-G-A | not specified | Uncertain significance (May 18, 2022) | ||
| 12-104757609-G-A | CHST11-related disorder | Likely benign (Feb 09, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHST11 | protein_coding | protein_coding | ENST00000303694 | 3 | 306720 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.406 | 0.592 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.84 | 146 | 223 | 0.654 | 0.0000147 | 2322 |
| Missense in Polyphen | 44 | 87.019 | 0.50564 | 838 | ||
| Synonymous | 0.835 | 84 | 94.3 | 0.891 | 0.00000664 | 675 |
| Loss of Function | 2.69 | 3 | 13.8 | 0.218 | 7.61e-7 | 153 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000626 | 0.0000615 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Can also sulfate Gal residues in desulfated dermatan sulfate. Preferentially sulfates in GlcA->GalNAc unit than in IdoA->GalNAc unit. Does not form 4, 6- di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.;
- Disease
- DISEASE: Note=A chromosomal aberration involving CHST11 is found in B-cell chronic lymphocytic leukemias. Translocation t(12;14)(q23;q32) with IgH. {ECO:0000269|PubMed:15273723}.;
- Pathway
- Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Sulfate/Sulfite Metabolism;Sulfite oxidase deficiency;Spinal Cord Injury;Endochondral Ossification;Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;Metabolism
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- 0.314
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.69
Haploinsufficiency Scores
- pHI
- 0.308
- hipred
- Y
- hipred_score
- 0.692
- ghis
- 0.592
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.830
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chst11
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; immune system phenotype; respiratory system phenotype; embryo phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- chst11
- Affected structure
- motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- branchiness
Gene ontology
- Biological process
- chondrocyte development;respiratory gaseous exchange;post-embryonic development;carbohydrate biosynthetic process;chondroitin sulfate biosynthetic process;negative regulation of transforming growth factor beta receptor signaling pathway;polysaccharide localization;post-anal tail morphogenesis;regulation of cell population proliferation;embryonic digit morphogenesis;negative regulation of apoptotic process;developmental growth;embryonic viscerocranium morphogenesis
- Cellular component
- Golgi membrane;membrane;integral component of membrane
- Molecular function
- N-acetylgalactosamine 4-O-sulfotransferase activity;chondroitin 4-sulfotransferase activity;N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity