CHST14
carbohydrate sulfotransferase 14, the group of Sulfotransferases, membrane bound
Basic information
Region (hg38): 15:40470984-40473158
Previous symbols: [ "D4ST1" ]
Links
Phenotypes
GenCC
Source:
- Ehlers-Danlos syndrome, musculocontractural type (Supportive), mode of inheritance: AR
- Ehlers-Danlos syndrome, musculocontractural type 1 (Definitive), mode of inheritance: AR
- Ehlers-Danlos syndrome, musculocontractural type 1 (Strong), mode of inheritance: AR
- Ehlers-Danlos syndrome, musculocontractural type 1 (Strong), mode of inheritance: AR
- Ehlers-Danlos syndrome, musculocontractural type 1 (Definitive), mode of inheritance: AR
- Ehlers-Danlos syndrome, musculocontractural type 1 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ehlers-Danlos syndrome, musculocontractural type 1 | AR | Hematologic; Musculoskeletal; Ophthalmologic | Clinical issues relate to connective tissue fragility may affect multiple organs, and may include severe bleeding episodes (eg, after minor trauma), such that recognition may allow precautions and preventive measures, as well as rapid treatment in the case of bleeding; Medical treatment (eg, with oral dermatan sulfate) may be beneficial; Due to risk of glaucoma, surveillance may allow early management | Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Ophthalmologic | 9084938; 10766984; 11370633; 16158441; 20004762; 20503305; 20842734; 20533528; 21744491; 22581468; 22407744; 22987394; 23704329 |
ClinVar
This is a list of variants' phenotypes submitted to
- Cardiovascular_phenotype (262 variants)
- Ehlers-Danlos_syndrome,_musculocontractural_type (174 variants)
- not_provided (62 variants)
- Ehlers-Danlos_syndrome,_musculocontractural_type_1 (24 variants)
- not_specified (14 variants)
- Ehlers-Danlos_syndrome (7 variants)
- CHST14-related_disorder (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000130468.4. 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 | 148 | 155 | ||||
| missense | 185 | 16 | 210 | |||
| nonsense | 8 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 13 | 25 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 24 | 16 | 193 | 164 | 2 |
Highest pathogenic variant AF is 0.000019206558
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHST14 | protein_coding | protein_coding | ENST00000306243 | 1 | 2194 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.447 | 0.547 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.683 | 182 | 210 | 0.867 | 0.0000108 | 2370 |
| Missense in Polyphen | 57 | 66.339 | 0.85922 | 844 | ||
| Synonymous | 0.703 | 87 | 95.8 | 0.909 | 0.00000479 | 841 |
| Loss of Function | 2.31 | 2 | 9.83 | 0.203 | 5.21e-7 | 98 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| 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 dermatan sulfate. Plays a pivotal role in the formation of 4-0-sulfated IdoA blocks in dermatan sulfate. Transfers sulfate to the C-4 hydroxyl of beta1,4-linked GalNAc that is substituted with an alpha-linked iduronic acid (IdoUA) at the C-3 hydroxyl. Transfers sulfate more efficiently to GalNAc residues in -IdoUA-GalNAc-IdoUA- than in -GlcUA-GalNAc-GlcUA-sequences. Has preference for partially desulfated dermatan sulfate. Addition of sulfate to GalNAc may occur immediately after epimerization of GlcUA to IdoUA. Appears to have an important role in the formation of the cerebellar neural network during postnatal brain development. {ECO:0000269|PubMed:19661164}.;
- Pathway
- Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;dermatan sulfate biosynthesis (late stages);dermatan sulfate biosynthesis;Metabolism
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.574
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.313
- hipred
- Y
- hipred_score
- 0.516
- ghis
- 0.585
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.123
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chst14
- Phenotype
- reproductive system phenotype; 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); 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); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; skeleton 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); limbs/digits/tail phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- carbohydrate biosynthetic process;dermatan sulfate biosynthetic process;dermatan sulfate proteoglycan metabolic process
- Cellular component
- Golgi membrane;integral component of membrane;extracellular exosome
- Molecular function
- N-acetylgalactosamine 4-O-sulfotransferase activity;phosphate ion binding