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Gene

VARS2

valyl-tRNA synthetase 2, mitochondrial

Summary

Cytogenetic location
6p21.33
Coordinates
Chromosome 6: 30,914,238–30,926,459 (GRCh38)
Exons
30 exons across 12.2 kb
Protein
1,063 amino acids
Also known as
DKFZP434L1435, KIAA1885, G7a
Previous symbols
VARS2L, VARSL
MANE Select transcript
ENST00000676266.1NM_020442.6
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 report relevant to this gene

  • Primary Mitochondrial Disease

    • Combined Oxidative Phosphorylation Deficiency

      Disorders, usually caused by nuclear genes involved in mitochondrial protein production, that reduce several respiratory chain complexes at once and often cause severe multisystem disease in childhood.

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

      Knowing can end a diagnostic search and guide surveillance and supportive care.

How VARS2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where VARS2 sits. VARS2 and 32 genes near it on chromosome 6, from 30,420,349 to 31,420,348.Chromosome 66p21.33p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2730.6 Mb30.8 Mb31 Mb31.2 Mb31.4 MbHLA-E: 30,489,495–30,494,205, forward strandHLA-EGNL1: 30,541,212–30,556,603, reverse strandGNL1PRR3: 30,556,704–30,563,723, forward strandPRR3ABCF1: 30,571,383–30,597,179, forward strandABCF1PPP1R10: 30,600,400–30,618,612, reverse strandMRPS18B: 30,617,759–30,626,398, forward strandMRPS18BATAT1: 30,626,837–30,646,835, forward strandATAT1C6orf136: 30,647,003–30,653,225, forward strandDHX16: 30,652,469–30,673,059, reverse strandDHX16PPP1R18: 30,676,389–30,687,895, reverse strandNRM: 30,688,047–30,691,420, reverse strandNRMMDC1: 30,699,807–30,717,562, reverse strandMDC1TUBB: 30,717,435–30,725,538, forward strandTUBBFLOT1: 30,727,709–30,743,075, reverse strandFLOT1IER3: 30,743,199–30,744,555, reverse strandIER3DDR1: 30,876,421–30,900,978, forward strandDDR1GTF2H4: 30,907,517–30,914,119, forward strandGTF2H4VARS2: 30,914,238–30,926,459, forward strandVARS2SFTA2: 30,931,353–30,955,636, reverse strandSFTA2SFTA2-AS1: 30,934,523–30,938,824, forward strandSFTA2-AS1MUCL3: 30,940,973–30,954,221, forward strandMUC21: 30,983,718–30,989,903, forward strandMUC21MUC22: 31,010,474–31,036,882, forward strandMUC22C6orf15: 31,111,223–31,112,582, reverse strandC6orf15PSORS1C1: 31,114,750–31,140,092, forward strandPSORS1C1CDSN: 31,115,087–31,120,446, reverse strandCDSNPSORS1C2: 31,137,534–31,139,721, reverse strandPSORS1C2CCHCR1: 31,142,439–31,158,238, reverse strandTCF19: 31,158,331–31,167,252, forward strandPOU5F1: 31,163,193–31,180,731, reverse strandPOU5F1HLA-C: 31,268,746–31,272,171, reverse strandHLA-CHLA-B: 31,353,195–31,367,067, reverse strandHLA-BMICA: 31,399,784–31,415,315, forward strandMICADiagram of VARS2: 30 exons on the forward strand of chromosome 6Exon 3: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 12: 1 known disease-causing siteExon 13: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 15: 4 known disease-causing sitesExon 17: 1 known disease-causing siteExon 20: 2 known disease-causing sitesExon 24: 1 known disease-causing siteExon 27: 2 known disease-causing sitesExon 28: 1 known disease-causing siteExon 1: 30,914,238–30,914,344, 107 basesExon 2: 30,914,810–30,915,037, 228 basesExon 3: 30,915,156–30,915,237, 82 basesExon 4: 30,915,355–30,915,455, 101 basesExon 5: 30,915,746–30,915,867, 122 basesExon 6: 30,915,981–30,916,047, 67 basesExon 7: 30,916,152–30,916,249, 98 basesExon 8: 30,916,878–30,916,959, 82 basesExon 9: 30,917,105–30,917,224, 120 basesExon 10: 30,917,695–30,917,806, 112 basesExon 11: 30,918,827–30,918,915, 89 basesExon 12: 30,919,758–30,919,848, 91 basesExon 13: 30,920,089–30,920,216, 128 basesExon 14: 30,920,333–30,920,436, 104 basesExon 15: 30,920,668–30,920,749, 82 basesExon 16: 30,921,065–30,921,141, 77 basesExon 17: 30,921,230–30,921,305, 76 basesExon 18: 30,921,589–30,921,691, 103 basesExon 19: 30,921,925–30,921,995, 71 basesExon 20: 30,922,116–30,922,241, 126 basesExon 21: 30,922,450–30,922,554, 105 basesExon 22: 30,922,706–30,922,774, 69 basesExon 23: 30,922,898–30,922,976, 79 basesExon 24: 30,923,104–30,923,231, 128 basesExon 25: 30,923,353–30,923,505, 153 basesExon 26: 30,924,354–30,924,560, 207 basesExon 27: 30,925,274–30,925,385, 112 basesExon 28: 30,925,544–30,925,719, 176 basesExon 29: 30,925,880–30,926,008, 129 basesExon 30: 30,926,109–30,926,459, 351 bases1246810121416182022242628305′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 3.6 kb of the gene's 12.2 kb; 3,192 of those bases code for the protein.

How a genome test reads VARS2

26

positions in VARS2 where ClinVar classes a change as pathogenic or likely pathogenic

26 of them (100%) fall in regions short reads find hard.

  • MHC (26 sites)The major histocompatibility complex (HLA genes), highly polymorphic and poorly represented by a single reference.

A whole genome covers all 12.2 kb of VARS2, introns included, not only the 3.6 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.). VARS2 gene: valyl-tRNA synthetase 2, mitochondrial. Retrieved 16 October 2026, from https://dantelabs.com/genes/vars2

Vancouver

Dante Labs. VARS2 gene: valyl-tRNA synthetase 2, mitochondrial [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/vars2

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