COMMD3
Basic information
Region (hg38): 10:22316386-22320306
Previous symbols: [ "C10orf8" ]
Links
Phenotypes
GenCC
Source:
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 COMMD3 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 | |||||
| missense | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in COMMD3
This is a list of pathogenic ClinVar variants found in the COMMD3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-22316423-G-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 10-22318820-T-G | not specified | Uncertain significance (Feb 22, 2023) | ||
| 10-22318964-T-C | not specified | Uncertain significance (May 25, 2022) | ||
| 10-22318977-T-C | not specified | Likely benign (Jun 16, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COMMD3 | protein_coding | protein_coding | ENST00000376836 | 8 | 4333 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000278 | 0.788 | 125604 | 0 | 144 | 125748 | 0.000573 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.346 | 113 | 103 | 1.10 | 0.00000496 | 1270 |
| Missense in Polyphen | 36 | 37.129 | 0.96961 | 510 | ||
| Synonymous | -1.73 | 52 | 38.3 | 1.36 | 0.00000187 | 360 |
| Loss of Function | 1.20 | 9 | 13.8 | 0.651 | 7.21e-7 | 157 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00609 | 0.00594 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000111 | 0.000109 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.000318 | 0.000316 |
| Middle Eastern | 0.000111 | 0.000109 |
| South Asian | 0.0000984 | 0.0000980 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). May down-regulate activation of NF-kappa-B (PubMed:15799966). Modulates Na(+) transport in epithelial cells by regulation of apical cell surface expression of amiloride-sensitive sodium channel (ENaC) subunits (PubMed:23637203). {ECO:0000269|PubMed:15799966, ECO:0000269|PubMed:23637203, ECO:0000305|PubMed:21778237}.;
- Pathway
- Neutrophil degranulation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Neddylation
(Consensus)
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.777
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.368
- hipred
- N
- hipred_score
- 0.322
- ghis
- 0.537
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.886
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Commd3
- Phenotype
Gene ontology
- Biological process
- sodium ion transport;neutrophil degranulation
- Cellular component
- extracellular region;nucleus;ficolin-1-rich granule lumen
- Molecular function
- protein binding