CHCHD3

coiled-coil-helix-coiled-coil-helix domain containing 3, the group of Protein phosphatase 1 regulatory subunits|Mitochondrial contact site and cristae organizing system subunits|Coiled-coil-helix-coiled-coil-helix domain containing proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 7:132784870-133082090

Links

ENSG00000106554

∙ NCBI:54927 ∙ OMIM:613748 ∙ HGNC:21906 ∙ Uniprot:Q9NX63 ∙ 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 CHCHD3 gene.

not_specified (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCHD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017812.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCHD3	protein_coding	protein_coding	ENST00000262570	8	297220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0275	0.970	125733	0	11	125744	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.369	114	126	0.907	0.00000685	1454
Missense in Polyphen		35	34.333	1.0194		477
Synonymous	0.666	40	45.7	0.875	0.00000240	412
Loss of Function	2.69	6	18.5	0.325	0.00000120	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

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. Has also been shown to function as a transcription factor which binds to the BAG1 promoter and represses BAG1 transcription. Plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology (PubMed:25781180). {ECO:0000269|PubMed:22567091, ECO:0000269|PubMed:25781180}.;
Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.551
rvis_EVS: 0.01
rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

pHI: 0.116
hipred: N
hipred_score: 0.492
ghis: 0.578

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.579

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Chchd3
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;inner mitochondrial membrane organization;mitochondrial fusion;cristae formation
Cellular component: nucleus;cytoplasm;mitochondrion;mitochondrial inner membrane;MICOS complex;extracellular exosome
Molecular function: DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;phosphatase binding;protein-containing complex scaffold activity