AARSD1
protein-codingalanyl-tRNA synthetase domain containing 1
Gene summary
Predicted to enable Ser-tRNA(Ala) deacylase activity. Predicted to be involved in regulation of translational fidelity. Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to AARSD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001261434.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 51 | 3 | 54 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 4 | 0 | 55 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001248363.1 | 12 | MANE Select | |
| Ensembl | ENSP00000400870.1 | 12 | MANE Select | |
| Ensembl | ENSP00000400735.2 | 5 | Standard | |
| Ensembl | ENSP00000404894.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- alanyl-tRNA aminoacylation
- regulation of translational fidelity
- biological_process
- aminoacyl-tRNA metabolism involved in translational fidelity
Molecular Function
- Ser-tRNA(Ala) hydrolase activity
- molecular_function
- nucleic acid binding
- alanine-tRNA ligase activity
- ATP binding
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000427569
- Coding exons
- 12
- Length
- 13973
- Individuals with no LoFs
- 125513
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 235
- Defined
- 125748
- p
- 0.000935
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.00928 | 243 | 243 | 0.998 | 0.0000136 | 2699 |
| Missense (PolyPhen) | 50 | 56.694 | 0.88192 | 609 | ||
| Synonymous | -0.165 | 94 | 92.0 | 1.02 | 0.00000485 | 823 |
| Loss of Function | 1.18 | 16 | 21.9 | 0.729 | 0.00000102 | 253 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0069 | 0.0069 | notable |
| Latino/Admixed American | 0.00078 | 0.00078 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00029 | 0.00029 | rare |
| South Asian | 0.0017 | 0.0017 | notable |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions in trans to edit the amino acid moiety from incorrectly charged tRNA(Ala). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0878
Intolerance Scores
- LoFtool
- 0.310
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.78
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0537