RARS1
Basic information
Region (hg38): 5:168486451-168519301
Previous symbols: [ "RARS" ]
Links
Phenotypes
GenCC
Source:
- hypomyelinating leukodystrophy 9 (Moderate), mode of inheritance: AR
- hypomyelinating leukodystrophy 9 (Supportive), mode of inheritance: AR
- hypomyelinating leukodystrophy 9 (Limited), mode of inheritance: Unknown
- hypomyelinating leukodystrophy 9 (Strong), mode of inheritance: AR
- hypomyelinating leukodystrophy 9 (Moderate), mode of inheritance: AR
- hypomyelinating leukodystrophy 9 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Leukodystrophy, hypomyelinating 9 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 24777941 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (246 variants)
- Inborn_genetic_diseases (87 variants)
- Hypomyelinating_leukodystrophy_9 (33 variants)
- not_specified (17 variants)
- RARS1-related_disorder (10 variants)
- Leukodystrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RARS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002887.4. 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 | 42 | 44 | ||||
missense | 141 | 10 | 156 | |||
nonsense | 9 | |||||
start loss | 3 | 1 | 4 | |||
frameshift | 12 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
Total | 17 | 15 | 143 | 52 | 2 |
Highest pathogenic variant AF is 0.0000282251
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RARS1 | protein_coding | protein_coding | ENST00000231572 | 15 | 32855 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.27e-8 | 0.997 | 125671 | 0 | 77 | 125748 | 0.000306 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.544 | 319 | 348 | 0.918 | 0.0000175 | 4343 |
Missense in Polyphen | 138 | 154.64 | 0.8924 | 1891 | ||
Synonymous | 0.192 | 116 | 119 | 0.978 | 0.00000547 | 1210 |
Loss of Function | 2.64 | 18 | 34.8 | 0.517 | 0.00000188 | 437 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000849 | 0.000842 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000437 | 0.000435 |
Finnish | 0.000370 | 0.000370 |
European (Non-Finnish) | 0.000316 | 0.000299 |
Middle Eastern | 0.000437 | 0.000435 |
South Asian | 0.000202 | 0.000196 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis (PubMed:25288775). Modulates the secretion of AIMP1 and may be involved in generation of the inflammatory cytokine EMAP2 from AIMP1 (PubMed:17443684). {ECO:0000269|PubMed:17443684, ECO:0000269|PubMed:25288775}.;
- Disease
- DISEASE: Leukodystrophy, hypomyelinating, 9 (HLD9) [MIM:616140]: An autosomal recessive neurodegenerative disorder characterized by delayed psychomotor development, severe spasticity, nystagmus, and ataxia associated with diffuse hypomyelination apparent on brain MRI. {ECO:0000269|PubMed:24777941}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Aminoacyl-tRNA biosynthesis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Amino Acid metabolism;tRNA Aminoacylation;Translation;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism;tRNA charging;Selenoamino acid metabolism;Arginine Proline metabolism;SeMet incorporation into proteins;Cytosolic tRNA aminoacylation
(Consensus)
Recessive Scores
- pRec
- 0.412
Intolerance Scores
- loftool
- 0.872
- rvis_EVS
- -0.42
- rvis_percentile_EVS
- 25.64
Haploinsufficiency Scores
- pHI
- 0.523
- hipred
- Y
- hipred_score
- 0.652
- ghis
- 0.611
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rars
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- tRNA aminoacylation for protein translation;arginyl-tRNA aminoacylation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;membrane;aminoacyl-tRNA synthetase multienzyme complex;extracellular exosome
- Molecular function
- tRNA binding;arginine-tRNA ligase activity;protein binding;ATP binding;arginine binding;cadherin binding