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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 10 | 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 | 10 | 0 | 0 |
Variants in CHCHD3
This is a list of pathogenic ClinVar variants found in the CHCHD3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-132785644-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 7-132796500-G-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 7-132796519-G-A | not specified | Uncertain significance (May 23, 2023) | ||
| 7-132885667-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 7-132885720-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 7-132885745-C-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 7-132975180-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 7-132975188-C-T | not specified | Uncertain significance (Dec 05, 2022) | ||
| 7-132975213-C-T | not specified | Uncertain significance (Mar 28, 2024) | ||
| 7-132975279-G-C | not specified | Uncertain significance (Mar 28, 2022) | ||
| 7-133024559-C-T | not specified | Uncertain significance (Apr 12, 2022) | ||
| 7-133070156-G-A | not specified | Uncertain significance (Apr 27, 2024) | ||
| 7-133070192-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 7-133070207-C-T | not specified | Uncertain significance (Aug 28, 2023) |
GnomAD
Source:
| 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:
- 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