CHCHD5

coiled-coil-helix-coiled-coil-helix domain containing 5, the group of Coiled-coil-helix-coiled-coil-helix domain containing proteins

Basic information

Region (hg38): 2:112584240-112589275

Previous symbols: [ "C2orf9" ]

Links

ENSG00000125611 ∙ NCBI:84269 ∙ OMIM:616978 ∙ HGNC:17840 ∙ Uniprot:Q9BSY4 ∙ 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 CHCHD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCHD5 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			6	2		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	0

Variants in CHCHD5

This is a list of pathogenic ClinVar variants found in the CHCHD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112586065-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-112586089-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-112586099-A-G		not specified	Likely benign (Dec 27, 2023)
2-112586236-G-T		not specified	Uncertain significance (Mar 30, 2024)
2-112586270-A-C		not specified	Uncertain significance (Oct 30, 2023)
2-112586306-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-112586316-T-G		not specified	Uncertain significance (Jun 16, 2023)
2-112586322-G-T		not specified	Uncertain significance (Oct 26, 2022)
2-112586340-C-T		not specified	Likely benign (Oct 18, 2021)
2-112588884-T-A		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCHD5	protein_coding	protein_coding	ENST00000324913	4	5036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0500	0.867	125719	0	22	125741	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.422	88	77.5	1.13	0.00000542	708
Missense in Polyphen		33	26.984	1.2229		271
Synonymous	0.398	26	28.7	0.906	0.00000193	218
Loss of Function	1.44	3	7.15	0.420	3.72e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000434	0.000434
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Intolerance Scores

• loftool: 0.552
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.0517
• hipred: N
• hipred_score: 0.170
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.644

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chchd5

Gene ontology

• Cellular component: mitochondrial intermembrane space