ARL4A
Basic information
Region (hg38): 7:12686856-12690958
Previous symbols: [ "ARL4" ]
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 ARL4A 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in ARL4A
This is a list of pathogenic ClinVar variants found in the ARL4A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-12688292-C-G | not specified | Uncertain significance (May 12, 2024) | ||
| 7-12688310-A-G | not specified | Uncertain significance (Aug 14, 2023) | ||
| 7-12688340-A-C | not specified | Uncertain significance (Mar 25, 2024) | ||
| 7-12688645-A-G | not specified | Uncertain significance (Mar 23, 2023) | ||
| 7-12688687-T-C | not specified | Uncertain significance (Apr 06, 2022) | ||
| 7-12688829-T-C | not specified | Uncertain significance (Apr 04, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARL4A | protein_coding | protein_coding | ENST00000396663 | 1 | 4079 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.805 | 0.190 | 125580 | 0 | 2 | 125582 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.461 | 87 | 100 | 0.870 | 0.00000452 | 1294 |
| Missense in Polyphen | 19 | 36.48 | 0.52084 | 481 | ||
| Synonymous | -0.217 | 40 | 38.3 | 1.04 | 0.00000176 | 396 |
| Loss of Function | 2.16 | 0 | 5.41 | 0.00 | 2.24e-7 | 83 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000336 | 0.0000327 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). GTP-binding protein that does not act as an allosteric activator of the cholera toxin catalytic subunit. Recruits CYTH1, CYTH2, CYTH3 and CYTH4 to the plasma membrane in GDP-bound form. {ECO:0000269|PubMed:10980193, ECO:0000269|PubMed:17398095}.;
- Pathway
- Mesodermal Commitment Pathway
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.225
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.529
- hipred
- Y
- hipred_score
- 0.503
- ghis
- 0.594
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arl4a
- Phenotype
- reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- intracellular protein transport;vesicle-mediated transport
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;plasma membrane
- Molecular function
- protein binding;GTP binding