CHCHD1

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

Basic information

Region (hg38): 10:73782047-73783652

Previous symbols: [ "C10orf34" ]

Links

ENSG00000172586 ∙ NCBI:118487 ∙ OMIM:608842 ∙ HGNC:23518 ∙ Uniprot:Q96BP2 ∙ 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 CHCHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCHD1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in CHCHD1

This is a list of pathogenic ClinVar variants found in the CHCHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73782085-C-T		not specified	Uncertain significance (Oct 07, 2024)
10-73782094-C-T		not specified	Uncertain significance (Aug 28, 2023)
10-73782104-T-G		not specified	Uncertain significance (Apr 12, 2023)
10-73782146-A-G		not specified	Uncertain significance (Aug 21, 2023)
10-73782170-G-C		not specified	Uncertain significance (Apr 19, 2024)
10-73782346-T-G		not specified	Likely benign (Feb 05, 2024)
10-73783078-C-T		not specified	Uncertain significance (Nov 21, 2024)
10-73783086-A-G		not specified	Uncertain significance (Sep 26, 2024)
10-73783099-A-G		not specified	Uncertain significance (Dec 27, 2024)
10-73783172-A-C		not specified	Uncertain significance (Jan 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCHD1	protein_coding	protein_coding	ENST00000372833	3	1606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000674	0.162	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.730	53	70.2	0.755	0.00000318	762
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0809

Intolerance Scores

• loftool: 0.497
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.0787
• hipred: N
• hipred_score: 0.354
• ghis: 0.615

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chchd1

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: fibrillar center;nucleoplasm;mitochondrion;mitochondrial inner membrane;mitochondrial ribosome;cytosol
• Molecular function: RNA binding;protein binding