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Aliases for HARS2 Gene

Aliases for HARS2 Gene

  • Histidyl-TRNA Synthetase 2, Mitochondrial 2 3 5
  • Histidine TRNA Ligase 2, Mitochondrial (Putative) 2 3
  • HisRS 3 4
  • HARSL 3 4
  • HARSR 3 4
  • HO3 3 4
  • Histidyl-TRNA Synthetase 2, Mitochondrial (Putative) 3
  • Probable Histidyl-TRNA Synthetase, Mitochondrial 3
  • Probable Histidine--TRNA Ligase, Mitochondrial 3
  • Histidine-TRNA Ligase Homolog 3
  • Histidyl-TRNA Synthetase-Like 2
  • Histidine--TRNA Ligase-Like 4
  • Histidyl-TRNA Synthetase 4
  • Histidine Translase 3
  • HARS-Related 3
  • EC 4
  • PRLTS2 3

External Ids for HARS2 Gene

Previous HGNC Symbols for HARS2 Gene


Previous GeneCards Identifiers for HARS2 Gene

  • GC20P018556
  • GC20P018563
  • GC20P018516
  • GC05P140053
  • GC05P135216
  • GC05P140088
  • GC05P140095
  • GC05P140110
  • GC05P141419
  • GC05P141563
  • GC05P141665
  • GC05P141766
  • GC05P141866
  • GC05P141975
  • GC05P142075
  • GC05P142180

Summaries for HARS2 Gene

Entrez Gene Summary for HARS2 Gene

  • Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. The protein encoded by this gene is an enzyme belonging to the class II family of aminoacyl-tRNA synthetases. Functioning in the synthesis of histidyl-transfer RNA, the enzyme plays an accessory role in the regulation of protein biosynthesis. The gene is located in a head-to-head orientation with HARS on chromosome five, where the homologous genes likely share a bidirectional promoter. Mutations in this gene are associated with the pathogenesis of Perrault syndrome, which involves ovarian dysgenesis and sensorineural hearing loss. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

GeneCards Summary for HARS2 Gene

HARS2 (Histidyl-TRNA Synthetase 2, Mitochondrial) is a Protein Coding gene. Diseases associated with HARS2 include Perrault Syndrome 2 and Perrault Syndrome. Among its related pathways are tRNA Aminoacylation and Gene Expression. Gene Ontology (GO) annotations related to this gene include aminoacyl-tRNA ligase activity. An important paralog of this gene is HARS.

Gene Wiki entry for HARS2 Gene

Additional gene information for HARS2 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HARS2 Gene

Genomics for HARS2 Gene

GeneHancer (GH) Regulatory Elements for HARS2 Gene

Promoters and enhancers for HARS2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J140690 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 671.7 +0.1 123 2.4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B CBX5 HARS2 HARS ZMAT2 TMCO6 LOC102723915 APBB3 HDAC3 ANKHD1 SRA1 PCDHA4
GH05J140399 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 41.2 -289.4 -289397 4.7 CLOCK ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 ANKHD1 ANKHD1-EIF4EBP3 ENSG00000249637 PURA HARS2 PCDHB18P PCDHGA6 IK APBB3 PCDHGA7
GH05J140710 Promoter/Enhancer 1.6 Ensembl ENCODE 52 +19.6 19558 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142295 LOC105378198 VTRNA1-1 HARS2 ANKHD1 WDR55 LOC102723915 HDAC3 PCDHB18P PURA
GH05J140637 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 33.1 -52.4 -52420 2.8 HDGF PKNOX1 SMAD1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 TMCO6 HARS2 ANKHD1 WDR55 HDAC3 LOC102723915 SRA1 PURA MALINC1 VTRNA1-1
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 40.3 +27.7 27710 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HARS2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HARS2 gene promoter:
  • p53
  • PPAR-gamma2
  • PPAR-gamma1
  • Nkx2-5
  • SRF (504 AA)
  • YY1
  • SRF
  • Lmo2
  • NF-E2
  • PPAR-alpha

Genomic Locations for HARS2 Gene

Genomic Locations for HARS2 Gene
7,893 bases
Plus strand
7,880 bases
Plus strand

Genomic View for HARS2 Gene

Genes around HARS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HARS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HARS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HARS2 Gene

Proteins for HARS2 Gene

  • Protein details for HARS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable histidine--tRNA ligase, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B4DDY8

    Protein attributes for HARS2 Gene

    506 amino acids
    Molecular mass:
    56888 Da
    Quaternary structure:
    • Homodimer.

    Alternative splice isoforms for HARS2 Gene


neXtProt entry for HARS2 Gene

Post-translational modifications for HARS2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HARS2 Gene

Domains & Families for HARS2 Gene

Gene Families for HARS2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the class-II aminoacyl-tRNA synthetase family.
  • Belongs to the class-II aminoacyl-tRNA synthetase family.
genes like me logo Genes that share domains with HARS2: view

Function for HARS2 Gene

Molecular function for HARS2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).

Enzyme Numbers (IUBMB) for HARS2 Gene

Phenotypes From GWAS Catalog for HARS2 Gene

Gene Ontology (GO) - Molecular Function for HARS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0004812 aminoacyl-tRNA ligase activity IEA --
GO:0004821 histidine-tRNA ligase activity IDA,TAS --
GO:0005515 protein binding IPI 25416956
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with HARS2: view
genes like me logo Genes that share phenotypes with HARS2: view

Human Phenotype Ontology for HARS2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for HARS2

CRISPR Products

miRNA for HARS2 Gene

miRTarBase miRNAs that target HARS2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HARS2

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for HARS2 Gene

Localization for HARS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HARS2 Gene

Mitochondrion matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HARS2 gene
Compartment Confidence
mitochondrion 5
cytosol 3
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HARS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA,IEA --
GO:0005739 mitochondrion IDA 21464306
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with HARS2: view

Pathways & Interactions for HARS2 Gene

genes like me logo Genes that share pathways with HARS2: view

Pathways by source for HARS2 Gene

1 KEGG pathway for HARS2 Gene

Gene Ontology (GO) - Biological Process for HARS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation NAS 7755634
GO:0006418 tRNA aminoacylation for protein translation TAS --
GO:0006427 histidyl-tRNA aminoacylation IDA 21464306
GO:0032543 NOT mitochondrial translation IBA --
genes like me logo Genes that share ontologies with HARS2: view

No data available for SIGNOR curated interactions for HARS2 Gene

Drugs & Compounds for HARS2 Gene

(4) Drugs for HARS2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
Histidine Approved Nutra 50
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(2) Additional Compounds for HARS2 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
genes like me logo Genes that share compounds with HARS2: view

Transcripts for HARS2 Gene

Unigene Clusters for HARS2 Gene

Histidyl-tRNA synthetase 2, mitochondrial:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HARS2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HARS2 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15
SP1: - - - -
SP2: - - - - - - -
SP3: - - - - - -
SP4: - - -
SP5: - - - - -
SP6: -
SP7: - - - - - -
SP8: - - -
SP9: - -
SP10: - -

Relevant External Links for HARS2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HARS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HARS2 Gene

Protein differential expression in normal tissues from HIPED for HARS2 Gene

This gene is overexpressed in Heart (10.8) and Lung (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HARS2 Gene

Protein tissue co-expression partners for HARS2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HARS2 Gene:


SOURCE GeneReport for Unigene cluster for HARS2 Gene:


mRNA Expression by UniProt/SwissProt for HARS2 Gene:

Tissue specificity: A high level expression is seen in the heart, kidney and skeletal muscle while a lower level expression is seen in the brain and liver.

Evidence on tissue expression from TISSUES for HARS2 Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Skin(4.4)
  • Muscle(2.2)
  • Kidney(2)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HARS2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • outer ear
  • pituitary gland
  • skull
  • breast
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with HARS2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for HARS2 Gene

Orthologs for HARS2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HARS2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HARS2 34 33
  • 99.8 (n)
(Bos Taurus)
Mammalia HARS2 34 33
  • 89.66 (n)
(Canis familiaris)
Mammalia HARS2 34 33
  • 88.45 (n)
(Rattus norvegicus)
Mammalia Hars2 33
  • 85.24 (n)
(Mus musculus)
Mammalia Hars2 16 34 33
  • 84.99 (n)
(Monodelphis domestica)
Mammalia HARS2 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia HARS2 34
  • 66 (a)
(Gallus gallus)
Aves HARS2 33
  • 71.13 (n)
  • 63 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 65 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100488813 33
  • 71.65 (n)
(Danio rerio)
Actinopterygii hars 34
  • 62 (a)
fruit fly
(Drosophila melanogaster)
Insecta Aats-his 34
  • 47 (a)
(Caenorhabditis elegans)
Secernentea hars-1 34
  • 46 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HTS1 34
  • 40 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8844 34
  • 59 (a)
Species where no ortholog for HARS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HARS2 Gene

Gene Tree for HARS2 (if available)
Gene Tree for HARS2 (if available)
Evolutionary constrained regions (ECRs) for HARS2: view image

Paralogs for HARS2 Gene

Paralogs for HARS2 Gene

(2) SIMAP similar genes for HARS2 Gene using alignment to 9 proteins:

  • B4DQ67_HUMAN
  • C9JV49_HUMAN
  • D6R9M5_HUMAN
  • D6RB22_HUMAN
  • E9PG66_HUMAN
genes like me logo Genes that share paralogs with HARS2: view

Variants for HARS2 Gene

Sequence variations from dbSNP and Humsavar for HARS2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs113209109 uncertain-significance, Retinitis pigmentosa-deafness syndrome 140,691,368(+) G/A upstream_transcript_variant
rs140540222 likely-pathogenic, uncertain-significance, not provided, not specified 140,695,556(+) C/T 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs144588417 uncertain-significance, Retinitis pigmentosa-deafness syndrome 140,690,932(+) C/A/T upstream_transcript_variant
rs186043734 conflicting-interpretations-of-pathogenicity, uncertain-significance, not specified, Retinitis pigmentosa-deafness syndrome 140,691,655(+) C/G 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, missense_variant, upstream_transcript_variant
rs369183621 uncertain-significance, Retinitis pigmentosa-deafness syndrome 140,691,350(+) T/A/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HARS2 Gene

Variant ID Type Subtype PubMed ID
nsv830508 CNV loss 17160897

Variation tolerance for HARS2 Gene

Residual Variation Intolerance Score: 27.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HARS2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HARS2 Gene

Disorders for HARS2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for HARS2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
perrault syndrome 2
  • prlts2
perrault syndrome
  • gonadal dysgenesis, xx type
charcot-marie-tooth disease, axonal, type 2w
  • cmt2w
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search HARS2 in MalaCards View complete list of genes associated with diseases


  • Perrault syndrome 2 (PRLTS2) [MIM:614926]: A sex-influenced disorder characterized by sensorineural deafness in both males and females and ovarian dysgenesis in females. Affected females have primary amenorrhea, streak gonads, and infertility, whereas affected males show normal pubertal development and are fertile. {ECO:0000269 PubMed:21464306}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HARS2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HARS2: view

No data available for Genatlas for HARS2 Gene

Publications for HARS2 Gene

  1. Mutations in mitochondrial histidyl tRNA synthetase HARS2 cause ovarian dysgenesis and sensorineural hearing loss of Perrault syndrome. (PMID: 21464306) Pierce SB … King MC (Proceedings of the National Academy of Sciences of the United States of America 2011) 2 3 4 58
  2. A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS. (PMID: 7755634) O'Hanlon TP … Miller FW (Biochemical and biophysical research communications 1995) 2 3 4 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for HARS2 Gene

Sources for HARS2 Gene

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