CHCHD10

coiled-coil-helix-coiled-coil-helix domain containing 10, the group of Coiled-coil-helix-coiled-coil-helix domain containing proteins

Basic information

Region (hg38): 22:23765833-23767972

Previous symbols: [ "C22orf16" ]

Links

ENSG00000250479 ∙ NCBI:400916 ∙ OMIM:615903 ∙ HGNC:15559 ∙ Uniprot:Q8WYQ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant mitochondrial myopathy with exercise intolerance (Strong), mode of inheritance: AD
• lower motor neuron syndrome with late-adult onset (Strong), mode of inheritance: AD
• frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (Strong), mode of inheritance: AD
• amyotrophic lateral sclerosis (Supportive), mode of inheritance: AD
• frontotemporal dementia with motor neuron disease (Supportive), mode of inheritance: AD
• lower motor neuron syndrome with late-adult onset (Supportive), mode of inheritance: AD
• autosomal dominant mitochondrial myopathy with exercise intolerance (Supportive), mode of inheritance: AD
• frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (Strong), mode of inheritance: AD
• autosomal dominant mitochondrial myopathy with exercise intolerance (Limited), mode of inheritance: AD
• lower motor neuron syndrome with late-adult onset (Strong), mode of inheritance: AD
• mitochondrial disease (Definitive), mode of inheritance: AD
• frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopathy, isolated mitochondrial, autosomal dominant	AD	Cardiovascular; Musculoskeletal	Individuals have been described with cardiomyopathy, and awareness may allow medical management; Heart transplant has been described; The condition may manifest with muscle weakness, and medical management (with steroids) has been reported as beneficial	Musculoskeletal; Neurologic	9324076; 21715705; 24934289; 25113787; 25193783; 25428574; 35700042

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHCHD10 gene.

• Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance (59 variants)
• not provided (46 variants)
• Inborn genetic diseases (28 variants)
• Autosomal dominant mitochondrial myopathy with exercise intolerance;Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (25 variants)
• Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance;Lower motor neuron syndrome with late-adult onset (24 variants)
• Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (18 variants)
• Frontotemporal dementia and/or amyotrophic lateral sclerosis 2 (11 variants)
• Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Lower motor neuron syndrome with late-adult onset (8 variants)
• not specified (7 variants)
• Lower motor neuron syndrome with late-adult onset (7 variants)
• Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance (6 variants)
• Autosomal dominant mitochondrial myopathy with exercise intolerance (6 variants)
• CHCHD10-related condition (3 variants)
• Amyotrophic lateral sclerosis (1 variants)
• - (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCHD10 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			1	30	2	33
missense	2	1	72	9	1	85
nonsense			6			6
start loss			1			1
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region			5	7	2	14
non coding			2	17	10	29
Total	2	1	86	56	13

Variants in CHCHD10

This is a list of pathogenic ClinVar variants found in the CHCHD10 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-23765954-G-A			Likely benign (Oct 17, 2018)
22-23765999-C-T		CHCHD10-related disorder	Likely benign (Jun 22, 2021)
22-23766012-G-T		Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2	Uncertain significance (Oct 28, 2021)
22-23766024-G-A		Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2	Likely benign (Jan 17, 2024)
22-23766026-C-A		Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance;Lower motor neuron syndrome with late-adult onset	Uncertain significance (Nov 28, 2022)
22-23766029-G-A		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Uncertain significance (Nov 29, 2022)
22-23766029-G-C		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Uncertain significance (Jan 21, 2023)
22-23766033-AG-A		Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance;Lower motor neuron syndrome with late-adult onset	Likely benign (Aug 21, 2022)
22-23766038-G-A		Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2	Likely benign (Aug 21, 2022)
22-23766039-G-A		Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2	Likely benign (May 05, 2023)
22-23766040-G-A		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Likely benign (Jan 21, 2024)
22-23766041-G-C		Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2	Likely benign (May 05, 2023)
22-23766043-A-C		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Likely benign (Aug 21, 2022)
22-23766045-C-G		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Likely benign (Aug 21, 2022)
22-23766101-C-G		Autosomal dominant mitochondrial myopathy with exercise intolerance • Frontotemporal dementia and/or amyotrophic lateral sclerosis 2 • Lower motor neuron syndrome with late-adult onset	Benign (Jul 22, 2021)
22-23766110-C-T		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Likely benign (Dec 30, 2023)
22-23766111-G-A		Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance;Lower motor neuron syndrome with late-adult onset	Likely benign (Dec 12, 2023)
22-23766113-G-C		Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Lower motor neuron syndrome with late-adult onset	Likely benign (Oct 26, 2022)
22-23766117-C-G		Lower motor neuron syndrome with late-adult onset;Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2	Likely benign (Dec 11, 2023)
22-23766117-C-T		Autosomal dominant mitochondrial myopathy with exercise intolerance;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Lower motor neuron syndrome with late-adult onset	Likely benign (Jul 31, 2023)
22-23766127-C-T		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Uncertain significance (Jan 25, 2024)
22-23766129-A-G		Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance;Lower motor neuron syndrome with late-adult onset	Uncertain significance (Aug 22, 2023)
22-23766131-G-A		Inborn genetic diseases	Likely benign (Oct 25, 2023)
22-23766134-A-G		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance • Inborn genetic diseases • CHCHD10-related disorder	Likely benign (Jan 21, 2024)
22-23766135-G-T		Lower motor neuron syndrome with late-adult onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 2;Autosomal dominant mitochondrial myopathy with exercise intolerance	Uncertain significance (Aug 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCHD10	protein_coding	protein_coding	ENST00000484558	4	2610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000537	0.143	125343	0	22	125365	0.0000877

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.825	47	65.8	0.714	0.00000309	842
Missense in Polyphen		22	27.018	0.81429		322
Synonymous	-0.414	34	31.1	1.09	0.00000164	303
Loss of Function	-0.746	7	5.17	1.35	2.22e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000928	0.000923
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000201	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the maintenance of mitochondrial organization and mitochondrial cristae structure. {ECO:0000269|PubMed:24934289}.
• Disease: DISEASE: Spinal muscular atrophy, Jokela type (SMAJ) [MIM:615048]: An autosomal dominant, slowly progressive, lower motor neuron disease. SMAJ is characterized by adult-onset of muscle cramps and fasciculations affecting the proximal and distal muscles of the upper and lower limbs. The disorder results in weakness and mild muscle atrophy later in life. {ECO:0000269|PubMed:25428574}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myopathy, isolated mitochondrial, autosomal dominant (IMMD) [MIM:616209]: A mitochondrial myopathy presenting with severe exercise intolerance, progressive proximal weakness, and lactic acidemia. The disorder is slowly progressive, with later involvement of facial muscles, muscles of the upper limbs, and distal muscles. {ECO:0000269|PubMed:25193783}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.205
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chchd10
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: oxidative phosphorylation;mitochondrion organization;stabilization of membrane potential;protein-containing complex disassembly;protein localization to nucleus;mitochondrial nucleoid organization;positive regulation of release of cytochrome c from mitochondria;maintenance of synapse structure;positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;positive regulation of mitochondrial transcription;positive regulation of cristae formation;positive regulation of cytochrome-c oxidase activity
• Cellular component: nucleus;mitochondrion;mitochondrial intermembrane space;MICOS complex
• Molecular function: molecular_function;protein binding