CHCHD1

protein-coding

coiled-coil-helix-coiled-coil-helix domain containing 1, the group of Coiled-coil-helix-coiled-coil-helix domain containing proteins

Gene summary

Enables RNA binding activity. Predicted to be involved in mitochondrial translation. Located in fibrillar center; mitochondrion; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C10orf34

MANE transcript

NM_203298.3

Inheritance

—

ClinVar variants

U:16B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.29

Max pathogenic AF

—

Genomic locus

chr10:73,782,047-73,783,652

External References & Databases

Ensembl (ENSG00000172586)

Transcript & Mutation Effects

hg38 • Region Span ~1.6 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 CHCHD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203298.3. 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						0
missense			15 clinvar	1 clinvar		16
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	1	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203298.3	RefSeq	NP_976043.1	3	MANE Select
ENST00000372833.6	Ensembl	ENSP00000361923.5	3	MANE Select
ENST00000372837.3	Ensembl	ENSP00000361928.3	2	Standard
ENST00000372837.4	Ensembl	ENSP00000361928.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mitochondrial translation initiation
Translation
Metabolism of proteins
Mitochondrial translation elongation
Mitochondrial translation termination

Biological Process

mitochondrial translational elongation
mitochondrial translational termination

Molecular Function

RNA binding
protein binding

Cellular Component

fibrillar center
nucleoplasm
mitochondrion
mitochondrial inner membrane
mitochondrial ribosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372833
Coding exons: 3
Length: 1606
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125748
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.730	53	70.2	0.755	0.00000318	762
Missense (PolyPhen)		14	18.392	0.76119		216
Synonymous	0.120	28	28.8	0.972	0.00000132	236
Loss of Function	-0.618	7	5.44	1.29	3.17e-7	56

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0809

Intolerance Scores

LoFtool: 0.497
RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.903

Gene Damage Prediction

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