ARMCX3
Basic information
Region (hg38): X:101622797-101627843
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 ARMCX3 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 | 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 | 7 | 1 | 0 |
Variants in ARMCX3
This is a list of pathogenic ClinVar variants found in the ARMCX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-101624990-C-T | not specified | Uncertain significance (Aug 30, 2021) | ||
| X-101625007-G-C | not specified | Uncertain significance (Aug 01, 2022) | ||
| X-101625086-A-C | not specified | Uncertain significance (Nov 12, 2021) | ||
| X-101625113-A-T | not specified | Uncertain significance (Aug 16, 2021) | ||
| X-101625283-C-T | not specified | Uncertain significance (Feb 11, 2022) | ||
| X-101625338-C-A | not specified | Uncertain significance (Jan 13, 2023) | ||
| X-101625760-C-T | not specified | Likely benign (Dec 27, 2022) | ||
| X-101625965-G-A | not specified | Uncertain significance (Mar 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARMCX3 | protein_coding | protein_coding | ENST00000341189 | 1 | 5047 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.459 | 0.517 | 125120 | 0 | 3 | 125123 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 82 | 140 | 0.586 | 0.0000107 | 2498 |
| Missense in Polyphen | 37 | 83.803 | 0.44151 | 1497 | ||
| Synonymous | 0.403 | 46 | 49.6 | 0.927 | 0.00000356 | 754 |
| Loss of Function | 1.81 | 1 | 5.64 | 0.177 | 3.55e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000149 | 0.0000999 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000124 | 0.00000882 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000253 | 0.000164 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates mitochondrial aggregation and transport in axons in living neurons. May link mitochondria to the TRAK2- kinesin motor complex via its interaction with Miro and TRAK2. Mitochondrial distribution and dynamics is regulated through ARMCX3 protein degradation, which is promoted by PCK and negatively regulated by WNT1. Enhances the SOX10-mediated transactivation of the neuronal acetylcholine receptor subunit alpha-3 and beta-4 subunit gene promoters. {ECO:0000250|UniProtKB:Q8BHS6}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.445
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 62.74
Haploinsufficiency Scores
- pHI
- 0.292
- hipred
- N
- hipred_score
- 0.407
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Armcx3
- Phenotype
Gene ontology
- Biological process
- cellular protein localization;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;integral component of mitochondrial outer membrane
- Molecular function