CHCHD6

coiled-coil-helix-coiled-coil-helix domain containing 6, the group of Mitochondrial contact site and cristae organizing system subunits|Protein phosphatase 1 regulatory subunits|Coiled-coil-helix-coiled-coil-helix domain containing proteins

Basic information

Region (hg38): 3:126704240-126960420

Links

ENSG00000159685 ∙ NCBI:84303 ∙ OMIM:615634 ∙ HGNC:28184 ∙ Uniprot:Q9BRQ6 ∙ 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 CHCHD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCHD6 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	1
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	1

Variants in CHCHD6

This is a list of pathogenic ClinVar variants found in the CHCHD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-126727151-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-126727153-C-T		not specified	Uncertain significance (Nov 17, 2023)
3-126733197-A-T		not specified	Uncertain significance (Jan 03, 2024)
3-126733218-G-A		not specified	Likely benign (Nov 14, 2023)
3-126852683-C-T		not specified	Uncertain significance (Sep 14, 2022)
3-126852686-C-T		not specified	Uncertain significance (Dec 14, 2022)
3-126852717-G-A		not specified	Uncertain significance (Jun 17, 2024)
3-126852728-A-C		not specified	Uncertain significance (Oct 18, 2021)
3-126914683-G-A		not specified	Uncertain significance (Apr 08, 2022)
3-126914693-A-G		not specified	Uncertain significance (Apr 25, 2023)
3-126914744-C-A		not specified	Uncertain significance (Aug 30, 2021)
3-126957428-G-A			Benign (Jul 13, 2018)
3-126957453-G-C		not specified	Uncertain significance (Dec 15, 2023)
3-126957475-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-126957483-C-A		not specified	Uncertain significance (Nov 09, 2021)
3-126957484-C-A		not specified	Uncertain significance (Jun 18, 2021)
3-126957484-C-T		not specified	Likely benign (Sep 01, 2021)
3-126957529-G-A		not specified	Likely benign (Mar 28, 2024)
3-126957540-G-A		not specified	Likely benign (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCHD6	protein_coding	protein_coding	ENST00000290913	8	256187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.57e-9	0.128	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.616	160	140	1.15	0.00000825	1501
Missense in Polyphen		42	43.579	0.96377		521
Synonymous	-0.305	57	54.1	1.05	0.00000316	447
Loss of Function	0.137	13	13.5	0.960	6.58e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000664	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000110	0.000109
South Asian	0.000229	0.000229
Other	0.000510	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. {ECO:0000269|PubMed:22228767}.

Recessive Scores

• pRec: 0.0796

Intolerance Scores

• loftool: 0.905
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.65

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.180
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.847

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chchd6

Gene ontology

• Biological process: cellular response to DNA damage stimulus;cristae formation
• Cellular component: mitochondrion;mitochondrial inner membrane;cytosol;MICOS complex
• Molecular function: protein binding