CTHRC1

collagen triple helix repeat containing 1

Basic information

Region (hg38): 8:103371537-103382989

Links

ENSG00000164932 ∙ NCBI:115908 ∙ OMIM:610635 ∙ HGNC:18831 ∙ Uniprot:Q96CG8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Barrett esophagus (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the CTHRC1 gene.

• Inborn genetic diseases (16 variants)

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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	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)
8-103371773-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)

GnomAD

Source: gnomAD

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: dbNSFP

• 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