NARS1

protein-coding

asparaginyl-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]

Previous symbols:
  • NARS

MANE transcript

NM_004539.4

Inheritance

AR, AD

ClinVar variants

P:26U:181B:28

Top phenotype

Neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr18:57,600,656-57,622,213

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~21.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: G2P

complex neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: G2P

neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalitiesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030837

Submitter: Labcorp Genetics (formerly Invitae)

neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalitiesMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030837

Submitter: Ambry Genetics

neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalitiesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030837

Submitter: PanelApp Australia

neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100348

Submitter: Labcorp Genetics (formerly Invitae)

neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalitiesMODERATE

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).

neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalitiesMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0100348

Submitter: Ambry Genetics

neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalitiesMODERATE

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).

neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100348

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalitiesAD/AR

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

Refs: 32738225; 32788587Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NARS1 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 110
not specifiedTotal: 88
Neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalitiesTotal: 41
Neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalitiesTotal: 21
NARS1-related disorderTotal: 18
Neurodevelopmental disorderTotal: 2
Mitochondrial complex 1 deficiency, nuclear type 35Total: 1
See casesTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
18
clinvar
1
clinvar
22
missense
12
clinvar
159
clinvar
9
clinvar
180
nonsense
1
clinvar
6
clinvar
2
clinvar
9
start loss
0
frameshift
3
clinvar
2
clinvar
8
clinvar
13
splice donor/acceptor (+/-2bp)
2
clinvar
9
clinvar
11
Total422181271235

Highest pathogenic variant AF is 0.001128285

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004539.4RefSeqNP_004530.114MANE Select
ENST00000256854.10EnsemblENSP00000256854.414MANE Select
ENST00000540592.5EnsemblENSP00000442496.17Standard
ENST00000586807.5EnsemblENSP00000464988.17Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8282683090.8680.00001723578
Missense (PolyPhen)70102.070.685841138
Synonymous-0.3391181131.040.000006381023
Loss of Function2.622037.20.5370.00000244398

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.000150.00014rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish0.000190.00018rare
European (Non-Finnish)0.000240.00024rare
South Asian0.000360.00036rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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