GeneBe

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.

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.

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
20
clinvar
 20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 20 0 0

Variants in CHORDC1

This is a list of pathogenic ClinVar variants found in the CHORDC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
11-90202416-T-C not specified Uncertain significance (Oct 20, 2023)3144492
11-90202422-C-A not specified Uncertain significance (Apr 05, 2023)2521919
11-90202431-T-C not specified Uncertain significance (Nov 02, 2023)3144491
11-90202497-T-A not specified Uncertain significance (Jan 02, 2024)3144490
11-90202512-T-C not specified Uncertain significance (Jul 09, 2021)2236030
11-90202827-C-T not specified Uncertain significance (Sep 12, 2023)2602894
11-90202833-G-C not specified Uncertain significance (Oct 07, 2024)3492419
11-90203414-A-G not specified Uncertain significance (Feb 02, 2025)3833100
11-90206232-T-C not specified Uncertain significance (Oct 17, 2024)3492420
11-90211265-T-C not specified Uncertain significance (Dec 02, 2022)2332329
11-90211289-A-G not specified Uncertain significance (Mar 01, 2023)2492634
11-90211305-T-A not specified Uncertain significance (Aug 27, 2024)3492418
11-90211305-T-C not specified Uncertain significance (Jul 20, 2022)2302486
11-90211312-A-C not specified Uncertain significance (Jun 11, 2021)2232357
11-90214078-G-A not specified Uncertain significance (Feb 13, 2025)2346210
11-90218137-T-C not specified Uncertain significance (Mar 22, 2023)2528150
11-90218147-G-C not specified Uncertain significance (Apr 07, 2023)2535034
11-90222912-C-A not specified Uncertain significance (Jul 02, 2024)3492417
11-90222917-C-T not specified Uncertain significance (Jun 24, 2022)2336274
11-90222948-A-T not specified Uncertain significance (Feb 15, 2023)2469410
11-90222951-C-G not specified Uncertain significance (Mar 06, 2023)2494814

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CHORDC1protein_codingprotein_codingENST00000320585 1122205
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9020.09841257200281257480.000111
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7451361630.8360.000007232177
Missense in Polyphen3243.3490.73819607
Synonymous-1.206755.61.210.00000262566
Loss of Function3.61320.70.1450.00000104274

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001820.000181
Ashkenazi Jewish0.0003970.000397
East Asian0.0001640.000163
Finnish0.00009310.0000924
European (Non-Finnish)0.0001270.000123
Middle Eastern0.0001640.000163
South Asian0.000.00
Other0.0001650.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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