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Gene

RUNX2

RUNX family transcription factor 2

Summary

Cytogenetic location
6p21.1
Coordinates
Chromosome 6: 45,328,330–45,551,082 (GRCh38)
Exons
9 exons across 222.8 kb
Protein
521 amino acids
Also known as
AML3, PEBP2A1, PEBP2aA1
Previous symbols
CCD, CBFA1, CCD1
MANE Select transcript
ENST00000647337.2NM_001024630.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Cleidocranial Dysplasia

    • Cleidocranial dysplasia (RUNX2-related)Autosomal dominant

      The main form of cleidocranial dysplasia, caused by RUNX2 variants, with retained baby teeth, extra teeth and permanent teeth that fail to erupt.

      • 4 GenCC submitters rate it definitive or strong
      Actionability

      Early, planned dental and orthodontic care improves outcomes for the dental problems typical of the condition.

How RUNX2 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 RUNX2 sits. RUNX2 and 2 genes near it on chromosome 6, from 44,939,706 to 45,939,705.Chromosome 66p21.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2745 Mb45.2 Mb45.4 Mb45.6 Mb45.8 MbSUPT3H: 44,809,317–45,377,953, reverse strandSUPT3HRUNX2: 45,328,330–45,551,082, forward strandRUNX2CLIC5: 45,880,827–46,080,348, reverse strandCLIC5Diagram of RUNX2: 9 exons on the forward strand of chromosome 6Exon 3: 11 known disease-causing sitesExon 4: 12 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 7: 4 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 1: 45,328,330–45,328,460, 131 basesExon 2: 45,328,661–45,328,784, 124 basesExon 3: 45,422,593–45,422,957, 365 basesExon 4: 45,431,863–45,432,019, 157 basesExon 5: 45,437,947–45,438,051, 105 basesExon 6: 45,491,941–45,492,114, 174 basesExon 7: 45,512,246–45,512,407, 162 basesExon 8: 45,545,217–45,545,282, 66 basesExon 9: 45,546,827–45,551,082, 4,256 bases1595′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 222.8 kb; 1,566 of those bases code for the protein.

Sequencing RUNX2

45

positions in RUNX2 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 222.8 kb of RUNX2, introns included, not only the 5.5 kb of exons.

Traits linked to RUNX2

The Human Phenotype Ontology lists these as features of the rare conditions RUNX2 can cause. Each trait's page lists the other genes linked to it.

Abnormality of head or neck

Show 37 more traits

External links

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 2026-10-17: 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 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). RUNX2 gene: RUNX family transcription factor 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/runx2

Vancouver

Dante Labs. RUNX2 gene: RUNX family transcription factor 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/runx2

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