CTHRC1
collagen triple helix repeat containing 1
Basic information
Region (hg38): 8:103371538-103382989
Links
Phenotypes
GenCC
Source:
- Barrett esophagus (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Barrett esophagus/Esophageal adenocarcinoma | AD | Gastrointestinal; Oncologic | Awareness of disease risk may allow surveillance, preventive measures (eg, related to Barrett esophagus) and early treatment of malignancy, which may reduce morbidity and mortality | Gastrointestinal; Oncologic | 21791690 |
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 CTHRC1 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 | 0 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 0 |
Variants in CTHRC1
This is a list of pathogenic ClinVar variants found in the CTHRC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-103371660-C-G | not specified | Uncertain significance (May 18, 2022) | ||
| 8-103371661-G-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 8-103371717-C-G | not specified | Uncertain significance (Sep 14, 2023) | ||
| 8-103371742-G-C | not specified | Uncertain significance (Mar 16, 2024) | ||
| 8-103371759-A-G | not specified | Uncertain significance (Mar 31, 2024) | ||
| 8-103371773-G-C | not specified | Uncertain significance (May 26, 2023) | ||
| 8-103371774-G-A | not specified | Uncertain significance (Aug 12, 2022) | ||
| 8-103371787-A-C | Barrett esophagus/esophageal adenocarcinoma | Pathogenic (Jul 27, 2011) | ||
| 8-103371788-G-C | not specified | Uncertain significance (Aug 10, 2021) | ||
| 8-103371790-G-A | not specified | Uncertain significance (Nov 12, 2021) | ||
| 8-103375781-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 8-103375837-G-A | not specified | Uncertain significance (Jul 05, 2022) | ||
| 8-103375878-C-G | not specified | Uncertain significance (Apr 12, 2022) | ||
| 8-103375882-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 8-103375958-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 8-103378078-A-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| 8-103378079-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 8-103378120-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 8-103378121-G-A | Uncertain significance (-) | |||
| 8-103378196-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 8-103378231-C-T | not specified | Uncertain significance (Mar 08, 2024) | ||
| 8-103382507-C-G | not specified | Uncertain significance (Jun 05, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTHRC1 | protein_coding | protein_coding | ENST00000330295 | 4 | 11483 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000267 | 0.546 | 125696 | 1 | 51 | 125748 | 0.000207 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.633 | 107 | 127 | 0.842 | 0.00000687 | 1525 |
| Missense in Polyphen | 35 | 45.967 | 0.76142 | 460 | ||
| Synonymous | 0.161 | 44 | 45.4 | 0.970 | 0.00000221 | 504 |
| Loss of Function | 0.659 | 8 | 10.3 | 0.778 | 4.83e-7 | 136 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000644 | 0.000644 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000924 | 0.000870 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000888 | 0.0000879 |
| Middle Eastern | 0.000924 | 0.000870 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000328 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: May act as a negative regulator of collagen matrix deposition. {ECO:0000250}.;
- Disease
- DISEASE: Barrett esophagus (BE) [MIM:614266]: A condition characterized by a metaplastic change in which normal esophageal squamous epithelium is replaced by a columnar and intestinal-type epithelium. Patients with Barrett esophagus have an increased risk of esophageal adenocarcinoma. The main cause of Barrett esophagus is gastroesophageal reflux. The retrograde movement of acid and bile salts from the stomach into the esophagus causes prolonged injury to the esophageal epithelium and induces chronic esophagitis, which in turn is believed to trigger the pathologic changes. {ECO:0000269|PubMed:21791690}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Noncanonical Wnt signaling pathway;Wnt signaling network
(Consensus)
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- loftool
- 0.651
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.240
- hipred
- N
- hipred_score
- 0.398
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.245
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cthrc1
- Phenotype
- hearing/vestibular/ear 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; liver/biliary system phenotype; embryo phenotype; normal phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- cell migration;positive regulation of protein binding;positive regulation of osteoblast proliferation;ossification involved in bone remodeling;positive regulation of osteoblast differentiation;Wnt signaling pathway, planar cell polarity pathway;inner ear receptor cell stereocilium organization;negative regulation of canonical Wnt signaling pathway;cochlea morphogenesis;establishment of planar polarity involved in neural tube closure
- Cellular component
- extracellular region;collagen trimer;extracellular space;cytoplasm;collagen-containing extracellular matrix
- Molecular function
- frizzled binding;extracellular matrix structural constituent;Wnt-protein binding