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Gene

HARS1

histidyl-tRNA synthetase 1

Summary

Cytogenetic location
5q31.3
Coordinates
Chromosome 5: 140,673,905–140,691,370 (GRCh38)
Exons
13 exons across 17.5 kb
Protein
509 amino acids
Inheritance
Autosomal recessive
Also known as
HisRS
Previous symbols
USH3B, HARS
MANE Select transcript
ENST00000504156.7NM_002109.6
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Usher Syndrome

    • Autosomal recessive

      A group of recessive conditions (types 1 to 4) causing sensorineural hearing loss, progressive retinitis pigmentosa and, in some types, balance problems, linked to genes such as USH2A, MYO7A, CDH23, PCDH15, USH1C, USH1G, ADGRV1, WHRN, CLRN1 and ARSG.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      An early diagnosis helps with decisions about the timing of cochlear implants, eye monitoring and eligibility for retinal therapy trials, and is relevant to carrier screening.

Broader groupings

  • Charcot-Marie-Tooth Disease

    • One of 62 genes linked to it

      A group of inherited peripheral neuropathies causing progressive weakness and wasting of the distal muscles and loss of sensation, mainly in the feet and hands.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Genetic counseling, subtype-specific monitoring, physical therapy, orthotics, neurotoxic drug avoidance, gene-specific clinical trials, surveillance for associated features

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How HARS1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 5, with a bracket where HARS1 sits. HARS1 and 43 genes near it on chromosome 5, from 140,182,638 to 141,182,637.Chromosome 55q31.3p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3140.2 Mb140.4 Mb140.6 Mb140.8 Mb141 MbCYSTM1: 140,174,924–140,282,212, forward strandCYSTM1PFDN1: 140,234,986–140,303,119, reverse strandPFDN1HBEGF: 140,332,843–140,346,614, reverse strandHBEGFSLC4A9: 140,360,188–140,375,324, forward strandSLC4A9ANKHD1: 140,401,660–140,541,168, forward strandANKHD1-EIF4EBP3: 140,401,908–140,549,569, forward strandSRA1: 140,536,450–140,557,920, reverse strandEIF4EBP3: 140,547,616–140,551,708, forward strandEIF4EBP3APBB3: 140,558,268–140,564,781, reverse strandAPBB3SLC35A4: 140,564,440–140,569,215, forward strandSLC35A4SURMIR: 140,564,440–140,569,215, forward strandSURMIRCD14: 140,630,402–140,633,711, reverse strandNDUFA2: 140,638,740–140,647,823, reverse strandTMCO6: 140,639,396–140,647,730, forward strandIK: 140,647,058–140,662,480, forward strandIKWDR55: 140,664,476–140,674,124, forward strandWDR55DND1: 140,670,794–140,673,576, reverse strandDND1HARS1: 140,673,905–140,691,370, reverse strandHARS1HARS2: 140,691,422–140,699,315, forward strandHARS2ZMAT2: 140,698,680–140,707,729, forward strandPCDHA1: 140,786,136–141,012,351, forward strandPCDHA1PCDHA2: 140,794,845–141,012,351, forward strandPCDHA2PCDHA3: 140,801,018–141,012,351, forward strandPCDHA3PCDHA4: 140,807,037–141,012,347, forward strandPCDHA4PCDHA5: 140,821,599–141,012,347, forward strandPCDHA6: 140,827,958–141,012,351, forward strandPCDHA7: 140,834,231–141,012,351, forward strandPCDHA8: 140,841,185–141,012,351, forward strandPCDHA9: 140,847,772–141,012,351, forward strandPCDHA10: 140,855,883–141,012,351, forward strandPCDHA11: 140,868,183–141,012,351, forward strandPCDHA12: 140,875,256–141,012,351, forward strandPCDHA13: 140,882,079–141,012,347, forward strandPCDHAC1: 140,926,299–141,012,351, forward strandPCDHAC2: 140,966,466–141,012,351, forward strandPCDHB1: 141,051,374–141,059,346, forward strandPCDHB1PCDHB2: 141,094,597–141,098,703, forward strandPCDHB2PCDHB3: 141,100,473–141,103,827, forward strandPCDHB3PCDHB4: 141,121,818–141,125,623, forward strandPCDHB4PCDHB5: 141,135,206–141,138,615, forward strandPCDHB5PCDHB6: 141,150,057–141,153,287, forward strandPCDHB7: 141,172,644–141,176,383, forward strandPCDHB7PCDHB8: 141,177,790–141,182,369, forward strandPCDHB8PCDHB16: 141,182,387–141,186,226, forward strandDiagram of HARS1: 13 exons on the reverse strand of chromosome 5Exon 12: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 5: 2 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 2: 1 known disease-causing siteExon 13: 140,673,905–140,674,328, 424 basesExon 12: 140,674,679–140,674,825, 147 basesExon 11: 140,675,017–140,675,133, 117 basesExon 10: 140,676,654–140,676,896, 243 basesExon 9: 140,676,989–140,677,116, 128 basesExon 8: 140,677,327–140,677,420, 94 basesExon 7: 140,677,655–140,677,753, 99 basesExon 6: 140,677,908–140,678,015, 108 basesExon 5: 140,679,002–140,679,127, 126 basesExon 4: 140,679,788–140,679,883, 96 basesExon 3: 140,683,100–140,683,219, 120 basesExon 2: 140,690,855–140,690,944, 90 basesExon 1: 140,691,215–140,691,370, 156 bases131210864215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.9 kb of the gene's 17.5 kb; 1,530 of those bases code for the protein.

How a genome test reads HARS1

11

positions in HARS1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 17.5 kb of HARS1, introns included, not only the 1.9 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). HARS1 gene: histidyl-tRNA synthetase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/hars1

Vancouver

Dante Labs. HARS1 gene: histidyl-tRNA synthetase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hars1

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