CHORDC1

cysteine and histidine rich domain containing 1

Basic information

Region (hg38): 11:90200429-90223077

Links

ENSG00000110172

∙ NCBI:26973 ∙ OMIM:604353 ∙ HGNC:14525 ∙ Uniprot:Q9UHD1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHORDC1 gene.

not_specified (31 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHORDC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012124.3. 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						0
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHORDC1	protein_coding	protein_coding	ENST00000320585	11	22205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.902	0.0984	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.745	136	163	0.836	0.00000723	2177
Missense in Polyphen		32	43.349	0.73819		607
Synonymous	-1.20	67	55.6	1.21	0.00000262	566
Loss of Function	3.61	3	20.7	0.145	0.00000104	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000164	0.000163
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Regulates centrosome duplication, probably by inhibiting the kinase activity of ROCK2. Proposed to act as co-chaperone for HSP90. May play a role in the regulation of NOD1 via a HSP90 chaperone complex. In vitro, has intrinsic chaperone activity. This function may be achieved by inhibiting association of ROCK2 with NPM1. Involved in stress response. Prevents tumorigenesis. {ECO:0000269|PubMed:20230755}.;
Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.455
rvis_EVS: 0.08
rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

pHI: 0.643
hipred: Y
hipred_score: 0.595
ghis: 0.534

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.233

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Chordc1
Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; neoplasm; hematopoietic 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype; immune system phenotype;

Gene ontology

Biological process: regulation of centrosome duplication;chaperone-mediated protein folding;regulation of cellular response to heat;negative regulation of Rho-dependent protein serine/threonine kinase activity
Cellular component: cellular_component
Molecular function: protein binding;ATP binding;zinc ion binding;ADP binding;Hsp90 protein binding