NARS2

asparaginyl-tRNA synthetase 2, mitochondrial, the group of Aminoacyl tRNA synthetases, Class II

Basic information

Region (hg38): 11:78435620-78575194

Previous symbols: [ "DFNB94" ]

Links

ENSG00000137513 ∙ NCBI:79731 ∙ OMIM:612803 ∙ HGNC:26274 ∙ Uniprot:Q96I59 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive 94 (Limited), mode of inheritance: AR
• combined oxidative phosphorylation defect type 24 (Strong), mode of inheritance: AR
• combined oxidative phosphorylation defect type 24 (Moderate), mode of inheritance: AD
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• combined oxidative phosphorylation defect type 24 (Supportive), mode of inheritance: AR
• mitochondrial disease (Moderate), mode of inheritance: AR
• hearing loss, autosomal recessive 94 (Limited), mode of inheritance: AR
• combined oxidative phosphorylation defect type 24 (Strong), mode of inheritance: AR
• Leigh syndrome (Limited), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 94	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Biochemical; Musculoskeletal; Neurologic	25385316; 25629079; 25807530

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NARS2 gene.

• not provided (4 variants)
• Combined oxidative phosphorylation defect type 24 (3 variants)
• Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NARS2 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			1	42	5	48
missense	1	4	94	5	4	108
nonsense	2	3	1			6
start loss			1			1
frameshift	2	2	1			5
inframe indel			2			2
splice donor/acceptor (+/-2bp)	2		1			3
splice region			4	15	2	21
non coding		1		62	41	104
Total	7	10	101	109	50

Highest pathogenic variant AF is 0.0000462

Variants in NARS2

This is a list of pathogenic ClinVar variants found in the NARS2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-78436471-G-A			Benign (Jun 25, 2018)
11-78436529-A-AT			Likely benign (Jun 26, 2018)
11-78436666-C-T			Benign (Aug 27, 2018)
11-78436683-G-A			Uncertain significance (Feb 28, 2022)
11-78436687-G-T		Inborn genetic diseases	Likely benign (Sep 13, 2023)
11-78436694-C-A			Uncertain significance (Dec 29, 2023)
11-78436719-A-G		NARS2-related primary mitochondrial disorder	Uncertain significance (Nov 02, 2021)
11-78436722-T-C		Inborn genetic diseases	Uncertain significance (May 26, 2023)
11-78436743-T-C		Combined oxidative phosphorylation defect type 24;Hearing loss, autosomal recessive 94	Uncertain significance (Apr 25, 2020)
11-78436752-C-T		Combined oxidative phosphorylation defect type 24	Uncertain significance (-)
11-78436754-T-C		NARS2-related disorder	Likely benign (Apr 08, 2019)
11-78436765-T-C		Sensorineural hearing loss disorder	Conflicting classifications of pathogenicity (Sep 28, 2021)
11-78436779-T-G			Uncertain significance (Feb 18, 2022)
11-78436789-A-G			Uncertain significance (Jul 31, 2023)
11-78436793-A-C			Uncertain significance (Jan 09, 2024)
11-78436797-C-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2022)
11-78436798-G-A		not specified	Uncertain significance (Jul 22, 2024)
11-78436798-G-C		Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Uncertain significance (May 03, 2020)
11-78436801-G-A		Combined oxidative phosphorylation defect type 24	Uncertain significance (Mar 08, 2019)
11-78436811-A-G			Likely benign (Oct 15, 2023)
11-78436813-A-G		Combined oxidative phosphorylation defect type 24 • NARS2-related disorder	Conflicting classifications of pathogenicity (Nov 24, 2023)
11-78436814-C-G		Combined oxidative phosphorylation defect type 24	Uncertain significance (Jun 08, 2022)
11-78436829-T-C			Likely benign (Dec 26, 2023)
11-78436831-G-C			Likely benign (Nov 28, 2021)
11-78436850-T-C			Likely benign (Sep 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NARS2	protein_coding	protein_coding	ENST00000281038	14	138913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.11e-8	0.974	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.759	292	258	1.13	0.0000131	3108
Missense in Polyphen		86	95.418	0.9013		1127
Synonymous	-1.04	100	87.6	1.14	0.00000397	915
Loss of Function	2.12	16	28.2	0.568	0.00000152	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000630	0.000630
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.0000674	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Combined oxidative phosphorylation deficiency 24 (COXPD24) [MIM:616239]: An autosomal recessive mitochondrial disorder with wide phenotypic variability. Some patients have a milder form affecting only skeletal muscle, whereas others may have a more severe disorder, reminiscent of Alpers syndrome. Alpers syndrome is a progressive neurodegenerative disorder that presents in infancy or early childhood and is characterized by diffuse degeneration of cerebral gray matter. {ECO:0000269|PubMed:25385316, ECO:0000269|PubMed:25629079}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leigh syndrome (LS) [MIM:256000]: An early-onset progressive neurodegenerative disorder characterized by the presence of focal, bilateral lesions in one or more areas of the central nervous system including the brainstem, thalamus, basal ganglia, cerebellum and spinal cord. Clinical features depend on which areas of the central nervous system are involved and include subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, and dysphagia. {ECO:0000269|PubMed:25807530}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
• Pathway: Aminoacyl-tRNA biosynthesis - Homo sapiens (human);Ectoderm Differentiation;tRNA Aminoacylation;Translation;Metabolism of proteins;tRNA charging;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Mitochondrial tRNA aminoacylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.42

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.492
• ghis: 0.602

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.759

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nars2

Gene ontology

• Biological process: asparaginyl-tRNA aminoacylation
• Cellular component: nucleoplasm;mitochondrion;mitochondrial matrix;cytosol
• Molecular function: nucleic acid binding;asparagine-tRNA ligase activity;ATP binding