AtlasGene
RUNX1
RUNX family transcription factor 1
- HGNC 10471↗(opens in a new tab)
- Ensembl gene ENSG00000159216↗(opens in a new tab)
- NCBI Gene 861↗(opens in a new tab)
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, 51.8 kDa
- Also known as
- PEBP2A2, AMLCR1
- Previous symbols
- AML1, CBFA2
- MANE Select transcript
- ENST00000675419.1NM_001754.5
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Inherited Predisposition to Acute Myeloid Leukaemia
- Autosomal dominant
Most AML arises from changes acquired in blood cells during life, but some people carry an inherited change in a predisposition gene. These include RUNX1 (familial platelet disorder), CEBPA, GATA2 deficiency, ANKRD26- and ETV6-related thrombocytopenia, and telomere biology genes TERT and TERC. A single changed copy is enough to raise risk.
- GenCC 11 GenCC submitter rates it definitive or strong
▶Actionability
Care is usually led by a haematologist, with regular blood count monitoring and a baseline bone marrow assessment where advised. Knowing the cause matters for stem cell transplant planning, as relatives who carry the same change should not be used as donors. Genetic counselling and testing of relatives are recommended.
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 definitiveClinGen rates the link definitive
- GenCC 66 GenCC submitters rate it definitive or strong
▶Actionability
Knowing about it supports regular blood count monitoring, and relatives offered as stem cell donors can be tested before donation.
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Get my Genome TestHow 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
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.
Sequencing RUNX1
6Easy
How hard RUNX1 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of RUNX1's exons sit where short reads map cleanly.
What adds to it: the share of RUNX1's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. On its own, a gene wholly in this kind of region would score 100.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. On its own, a gene wholly in this kind of region would score 60.0%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so a read from one may be placed on the other. On its own, a gene wholly in this kind of region would score 60.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. On its own, a gene wholly in this kind of region would score 50.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. On its own, a gene wholly in this kind of region would score 30.9.2%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. On its own, a gene wholly in this kind of region would score 20.18%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of RUNX1's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
185
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 (221)
The RUNX1 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | HGVS c. | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|---|
| A63Gfs*76 | c.184_187dup | Exon 4 | 34,887,006 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A65Rfs*73 | c.191_192insA | Exon 4 | 34,887,002 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A65Vfs*82 | c.166_193dup | Exon 4 | 34,887,000 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A83Gfs*55 | c.247dup | Exon 4 | 34,886,946 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A120Gfs*18 | c.356dup | Exon 5 | 34,880,708 | Likely pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A134P | c.400G>C | Exon 5 | 34,880,665 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A134Qfs*2 | c.400_404del | Exon 5 | 34,880,660 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A134T | c.400G>A | Exon 5 | 34,880,665 | Likely pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A134V | c.401C>T | Exon 5 | 34,880,664 | Likely pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| A142Gfs*2 | c.424dup | Exon 5 | 34,880,640 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
ClinVar pathogenic variants (230)
The RUNX1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 122
- Likely pathogenic 108
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_001754.5(RUNX1):c.1412_1413dup (p.Leu472fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.1242C>G (p.Tyr414Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.1117_1132del (p.Ser373fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.967+2_967+5del | hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.958C>T (p.Arg320Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.861C>A (p.Tyr287Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.861C>G (p.Tyr287Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.847C>T (p.Gln283Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.830del (p.Pro277fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.820C>T (p.Gln274Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.814C>T (p.Gln272Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.806-1G>A | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.802C>T (p.Gln268Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.796C>T (p.Gln266Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.784C>T (p.Gln262Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.777_778dup (p.Asn260fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.777dup (p.Asn260Ter) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.764_765del (p.His255fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.735del (p.Thr246fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.735dup (p.Thr246fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.723_729dup (p.Ala244fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.713_726del (p.Val238fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.719del (p.Pro240fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.698del (p.Arg233fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
| NM_001754.5(RUNX1):c.697del (p.Arg233fs) | hereditary thrombocytopenia and hematologic cancer predisposition syndrome | Pathogenic | ★★★★3 stars out of 4 reviewed by expert panel |
See all 230 with every other RUNX1 variant in ClinVar → (opens in a new tab)
Genes linked to the same conditions
- ETV6ETS variant transcription factor 6Shares 2 conditions
- ANKRD26ankyrin repeat domain 26Shares 1 condition
- CEBPACCAAT enhancer binding protein alphaShares 1 condition
- GATA2GATA binding protein 2Shares 1 condition
- TERCtelomerase RNA componentShares 1 condition
- TERTtelomerase reverse transcriptaseShares 1 condition
Traits linked to RUNX1
The Human Phenotype Ontology lists these as features of the rare conditions RUNX1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of blood and blood-forming tissues
- Abnormal dense granule content
- Acute monocytic leukemia
- Blood spots
- Ecchymosis
- Impaired ADP-induced platelet aggregation
- Impaired arachidonic acid-induced platelet aggregation
- Impaired collagen-induced platelet aggregation
- Impaired platelet aggregation
Show 23 more traits
- Low platelet count
- Myeloproliferative disorder
- Petechiae
- Prolonged bleeding time
- Abnormal mast cell morphology
- Abnormal basophil morphology
- Abnormal granulocyte morphology
- Abnormality of blood and blood-forming tissues
- Elevated white blood count
- Increased CD25+ mast cell proportion
- Increased number of platelets in blood
- Acute myeloid leukemia
- Blood cancer
- Blood tumor
- Gastrointestinal bleeding
- Low blood cell count
- Low blood neutrophil count
- Low number of red blood cells or hemoglobin
- Abnormal alpha granule content
- Bloody nose
- Bruising susceptibility
- Cancer of lymphatic system
- Myelodysplasia
External links
Gene records
Transcript
Protein
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 2026-10-23: 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 Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- AlphaFold DB model AF-Q01196-F1, version 6, from Google DeepMind and EMBL-EBI (CC BY 4.0): the protein's structure as AlphaFold predicts it, not as measured, and its confidence in each part.
- Data release 2026.10.23-dc0c0517.
Cite this page
Dante Labs. (n.d.). RUNX1 gene: RUNX family transcription factor 1. Retrieved 23 October 2026, from https://dantelabs.com/genes/runx1
Dante Labs. RUNX1 gene: RUNX family transcription factor 1 [Internet]. [cited 23 October 2026]. Available from: https://dantelabs.com/genes/runx1
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