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Gene

RUNX1

RUNX family transcription factor 1

Summary

Cytogenetic location
21q22.12
Coordinates
Chromosome 21: 34,787,801–35,049,302 (GRCh38)
Exons
9 exons across 261.5 kb
Protein
480 amino acids
Inheritance
Autosomal dominant
Also known as
PEBP2A2, AMLCR1
Previous symbols
AML1, CBFA2
MANE Select transcript
ENST00000675419.1NM_001754.5
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

  • Inherited Thrombocytopenias

    • Hereditary Thrombocytopenia with Blood Cancer PredispositionAutosomal dominant

      A dominant group of conditions, including RUNX1 familial platelet disorder, in which a low platelet count or poorly working platelets come with an increased lifetime risk of myeloid blood cancers such as myelodysplastic syndrome and acute myeloid leukaemia.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing about it supports regular blood count monitoring, and relatives offered as stem cell donors can be tested before donation.

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How RUNX1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 21, with a bracket where RUNX1 sits. RUNX1 and 5 genes near it on chromosome 21, from 34,418,552 to 35,418,551.Chromosome 2121q22.12p13p12p11.2p11.1q11.1q11.2q21.1q21.2q21.3q22.11q22.12q22.13q22.2q22.334.6 Mb34.8 Mb35 Mb35.2 Mb35.4 MbSMIM34: 34,414,494–34,423,951, reverse strandSMIM34KCNE1: 34,446,688–34,512,214, reverse strandKCNE1: 34,511,122–34,614,913, reverse strandRCAN1: 34,513,142–34,615,323, reverse strandRCAN1CLIC6: 34,668,966–34,718,227, forward strandCLIC6RUNX1: 34,787,801–35,049,302, reverse strandRUNX1Diagram of RUNX1: 9 exons on the reverse strand of chromosome 21Exon 9: 41 known disease-causing sitesExon 8: 13 known disease-causing sitesExon 7: 22 known disease-causing sitesExon 6: 23 known disease-causing sitesExon 5: 31 known disease-causing sitesExon 4: 40 known disease-causing sitesExon 9: 34,787,801–34,792,610, 4,810 bases. 44 variants with a page in exon 9. List themExon 8: 34,799,301–34,799,462, 162 bases. 15 variants with a page in exon 8. List themExon 7: 34,834,410–34,834,601, 192 bases. 25 variants with a page in exon 7. List themExon 6: 34,859,474–34,859,578, 105 bases. 29 variants with a page in exon 6. List themExon 5: 34,880,557–34,880,713, 157 bases. 39 variants with a page in exon 5. List themExon 4: 34,886,843–34,887,096, 254 bases. 46 variants with a page in exon 4. List themExon 3: 34,892,925–34,892,963, 39 basesExon 2: 35,048,842–35,048,958, 117 basesExon 1: 35,049,168–35,049,302, 135 bases9515′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 6 kb of the gene's 261.5 kb; 1,443 of those bases code for the protein.

How a genome test reads RUNX1

184

positions in RUNX1 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 261.5 kb of RUNX1, introns included, not only the 6 kb of exons.

Variants with a page (219)

The RUNX1 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A63Gfs*76c.184_187dupExon 434,887,006Pathogenic3 stars out of 4 reviewed by expert panel
A65Rfs*73c.191_192insAExon 434,887,002Pathogenic3 stars out of 4 reviewed by expert panel
A65Vfs*82c.166_193dupExon 434,887,000Pathogenic3 stars out of 4 reviewed by expert panel
A83Gfs*55c.247dupExon 434,886,946Pathogenic3 stars out of 4 reviewed by expert panel
A120Gfs*18c.356dupExon 534,880,708Likely pathogenic3 stars out of 4 reviewed by expert panel
A134Pc.400G>CExon 534,880,665Pathogenic3 stars out of 4 reviewed by expert panel
A134Qfs*2c.400_404delExon 534,880,660Pathogenic3 stars out of 4 reviewed by expert panel
A134Tc.400G>AExon 534,880,665Likely pathogenic3 stars out of 4 reviewed by expert panel
A134Vc.401C>TExon 534,880,664Likely pathogenic3 stars out of 4 reviewed by expert panel
A142Gfs*2c.424dupExon 534,880,640Pathogenic3 stars out of 4 reviewed by expert panel

See all 219 RUNX1 variants →

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.). RUNX1 gene: RUNX family transcription factor 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/runx1

Vancouver

Dante Labs. RUNX1 gene: RUNX family transcription factor 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/runx1

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