NARS1
protein-codingasparaginyl-tRNA synthetase 1, the group of Aminoacyl tRNA synthetases, Class II
Gene summary
Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. Asparaginyl-tRNA synthetase is localized to the cytoplasm and belongs to the class II family of tRNA synthetases. The N-terminal domain represents the signature sequence for the eukaryotic asparaginyl-tRNA synthetases. [provided by RefSeq, Jul 2008]
- NARS
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0100038
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0100038
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0030837
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0030837
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0030837
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0100348
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0100348
Submitter: ClinGen
The *NARS1* gene is located on chromosome 18 at 18q21.31 and encodes the cytoplasmic asparaginyl-tRNA synthetase that mediates the charging of the Asn amino acid onto its cognate transfer RNA, which is essential for protein synthesis. *NARS1* was first reported in relation to autosomal recessive neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities (NEDMILG) in 2020 (Manole et al., PMID: 32738225). NEDMILG is characterized by global developmental delay, delayed walking with variable gait abnormalities, impaired intellectual development with poor or absent speech and language, and progressive microcephaly. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in inheritance patterns during the precuration. Therefore, the following disease entities have been split into multiple disease entities, autosomal recessive (AR) neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities (OMIM:619091) and autosomal dominant (AD) neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities (NEDMILEG) (OMIM:619092). The split curation for AD NEDMILEG has been curated separately with evidence for AR NEDMILEG included here. Eight missense and one nonsense variants that have been reported in six probands in two publications (PMIDs: 32788587, 32738225) are included in this curation. The mechanism of pathogenicity is unknown at this time. This gene-disease relationship is also supported by expression studies, functional alteration of patient cells, and biochemical function (PMIDs: 32788587, 32738225, 32303649). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged.This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date March 6th, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0100348
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0030837
Submitter: ClinGen
The *NARS1* gene is located on chromosome 18 at 18q21.31 and encodes the cytoplasmic asparaginyl-tRNA synthetase that mediates the charging of the Asn amino acid onto its cognate transfer RNA, which is essential for protein synthesis. *NARS1* was first reported in relation to autosomal dominant neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities (NEDMILEG) in 2020 (Manole et al., PMID: 32738225). NEDMILEG is characterized by global developmental delay, delayed walking with variable gait abnormalities, impaired intellectual development with poor or absent speech and language, and progressive microcephaly. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in inheritance patterns during the precuration. Therefore, the following disease entities have been split into multiple disease entities, autosomal dominant (AD) neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities (NEDMILEG) (OMIM:619092) and autosomal recessive (AR) neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities (OMIM:619091). The split curation for AR NEDMILG has been curated separately with evidence for AD NEDMILG included here. Two missense and one nonsense variants that have been reported in eight probands in one publication (PMID: 32738225) are included in this curation. The mechanism of pathogenicity is unknown at this time. This gene-disease relationship is also supported by functional alteration of patient cells, a zebrafish model, and biochemical function (PMIDs: 32738225, 32303649). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged.This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date March 6th, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0100348
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NARS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004539.4. 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 | 3 | 18 | 1 | 22 | ||
| missense | 12 | 159 | 9 | 180 | ||
| nonsense | 1 | 6 | 2 | 9 | ||
| start loss | 0 | |||||
| frameshift | 3 | 2 | 8 | 13 | ||
| splice donor/acceptor (+/-2bp) | 2 | 9 | 11 | |||
| Total | 4 | 22 | 181 | 27 | 1 | 235 |
Highest pathogenic variant AF is 0.001128285
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004530.1 | 14 | MANE Select | |
| Ensembl | ENSP00000256854.4 | 14 | MANE Select | |
| Ensembl | ENSP00000442496.1 | 7 | Standard | |
| Ensembl | ENSP00000464988.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Aminoacyl-tRNA biosynthesis - Homo sapiens (human)
- Hypoacetylaspartia
- Aspartate Metabolism
- Canavan Disease
- miR-targeted genes in epithelium - TarBase
Biological Process
- tRNA aminoacylation for protein translation
- asparaginyl-tRNA aminoacylation
Molecular Function
- nucleic acid binding
- asparagine-tRNA ligase activity
- ATP binding
Cellular Component
- cytoplasm
- cytosol
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000256854
- Coding exons
- 14
- Length
- 21558
- Individuals with no LoFs
- 125696
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 52
- Defined
- 125748
- p
- 0.000207
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.828 | 268 | 309 | 0.868 | 0.0000172 | 3578 |
| Missense (PolyPhen) | 70 | 102.07 | 0.68584 | 1138 | ||
| Synonymous | -0.339 | 118 | 113 | 1.04 | 0.00000638 | 1023 |
| Loss of Function | 2.62 | 20 | 37.2 | 0.537 | 0.00000244 | 398 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00024 | 0.00024 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.150
Intolerance Scores
- LoFtool
- 0.493
- RVIS EVS
- -0.51
- RVIS percentile EVS
- 21.56
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |