CHCHD7

coiled-coil-helix-coiled-coil-helix domain containing 7, the group of Mitochondrial respiratory chain complex assembly factors|Coiled-coil-helix-coiled-coil-helix domain containing proteins

Basic information

Region (hg38): 8:56211686-56218809

Links

ENSG00000170791 ∙ NCBI:79145 ∙ OMIM:611238 ∙ HGNC:28314 ∙ Uniprot:Q9BUK0 ∙ 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 CHCHD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCHD7 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			7	3		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	3	0

Variants in CHCHD7

This is a list of pathogenic ClinVar variants found in the CHCHD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-56212854-A-G		not specified	Uncertain significance (Sep 03, 2024)
8-56212873-C-G		not specified	Uncertain significance (Dec 20, 2024)
8-56212883-G-C		not specified	Likely benign (Jan 29, 2025)
8-56216439-G-C		not specified	Uncertain significance (Oct 04, 2024)
8-56216447-C-T		not specified	Likely benign (Apr 08, 2024)
8-56216449-C-T		not specified	Uncertain significance (Dec 12, 2024)
8-56216484-A-G		not specified	Uncertain significance (Aug 14, 2024)
8-56216504-G-C		not specified	Uncertain significance (Jan 30, 2024)
8-56217337-A-G		not specified	Likely benign (Jul 12, 2022)
8-56217337-A-T		not specified	Uncertain significance (Jan 22, 2024)
8-56217340-G-A		not specified	Likely benign (Jan 31, 2023)
8-56217364-G-A		not specified	Uncertain significance (Aug 01, 2024)
8-56217383-C-T		not specified	Uncertain significance (Jul 26, 2024)
8-56217425-T-C		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCHD7	protein_coding	protein_coding	ENST00000303759	4	7113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0349	0.838	125700	0	42	125742	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.283	56	62.3	0.899	0.00000327	726
Missense in Polyphen		22	20.574	1.0693		234
Synonymous	-1.19	29	21.9	1.32	0.00000133	191
Loss of Function	1.21	3	6.28	0.478	2.64e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving CHCHD7 is found in salivary gland pleiomorphic adenomas, the most common benign epithelial tumors of the salivary gland. Translocation t(6;8)(p21.3-22;q13) with PLAG1. {ECO:0000269|PubMed:16736500}.
• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Intolerance Scores

• loftool: 0.297
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.199
• hipred: N
• hipred_score: 0.200
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chchd7

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;mitochondrial intermembrane space
• Molecular function: molecular_function