CHORDC1

protein-coding

cysteine and histidine rich domain containing 1

Gene summary

Enables Hsp90 protein binding activity. Predicted to be involved in several processes, including centrosome duplication; obsolete negative regulation of Rho-dependent protein serine/threonine kinase activity; and regulation of cellular response to heat. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_012124.3

Inheritance

—

ClinVar variants

U:42

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr11:90,200,429-90,223,077

External References & Databases

Ensembl (ENSG00000110172)

Transcript & Mutation Effects

hg38 • Region Span ~22.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHORDC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012124.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			35 clinvar			35
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	42	0	0	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012124.3	RefSeq	NP_036256.2	11	MANE Select
ENST00000320585.11	Ensembl	ENSP00000319255.6	11	MANE Select
NM_001144073.2	RefSeq	NP_001137545.1	10	Standard
ENST00000457199.6	Ensembl	ENSP00000401080.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

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

Molecular Function

protein binding
ATP binding
zinc ion binding
ADP binding
Hsp90 protein binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320585
Coding exons: 11
Length: 22205
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125748
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.745	136	163	0.836	0.00000723	2177
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.455
RVIS EVS: 0.08
RVIS percentile EVS: 59.76

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.233

Gene Damage Prediction

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