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Gene

HMGB1

high mobility group box 1

Summary

Cytogenetic location
13q12.3
Coordinates
Chromosome 13: 30,456,704–30,465,936 (GRCh38)
Exons
5 exons across 9.2 kb
Protein
215 amino acids
Also known as
HMG3, SBP-1, DKFZp686A04236
Previous symbols
HMG1
MANE Select transcript
ENST00000341423.10NM_002128.7
Locus type
gene with protein product

Reference genomeGRCh38

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

Curated reports relevant to this gene

No Genome Test report reads HMGB1 yet. The test sequences your whole genome, so your data includes it all the same.

How HMGB1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 13, with a bracket where HMGB1 sits. HMGB1 and 6 genes near it on chromosome 13, from 29,961,320 to 30,961,319.Chromosome 1313q12.3p13p12p11.2p11.1q11q12.11q12.12q12.13q12.2q12.3q13.1q13.2q13.3q14.11q14.12q14.13q14.2q14.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q3430 Mb30.2 Mb30.4 Mb30.6 Mb30.8 MbKATNAL1: 30,202,630–30,307,554, reverse strandKATNAL1UBE2L5: 30,422,488–30,429,758, forward strandUBE2L5HMGB1: 30,456,704–30,465,936, reverse strandHMGB1USPL1: 30,617,693–30,660,770, forward strandUSPL1ALOX5AP: 30,713,478–30,765,072, forward strandALOX5APMEDAG: 30,906,200–30,925,574, forward strandMEDAGTEX26: 30,932,639–30,982,522, forward strandTEX26Diagram of HMGB1: 5 exons on the reverse strand of chromosome 13Exon 5: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 5: 30,456,704–30,461,533, 4,830 basesExon 4: 30,462,538–30,462,712, 175 basesExon 3: 30,463,207–30,463,352, 146 basesExon 2: 30,463,531–30,463,694, 164 basesExon 1: 30,465,796–30,465,936, 141 bases543215′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 5.5 kb of the gene's 9.2 kb; 648 of those bases code for the protein.

How a genome test reads HMGB1

2

positions in HMGB1 where ClinVar classes a change as pathogenic or likely pathogenic

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

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (1 site)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 9.2 kb of HMGB1, introns included, not only the 5.5 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.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). HMGB1 gene: high mobility group box 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/hmgb1

Vancouver

Dante Labs. HMGB1 gene: high mobility group box 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/hmgb1

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