Gene Gene information from NCBI Gene database.
Entrez ID 860
Gene name RUNX family transcription factor 2
Gene symbol RUNX2
Synonyms (NCBI Gene)
AML3CBF-alpha-1CBFA1CCDCCD1CLCDOSF-2OSF2PEA2aAPEBP2aA
Chromosome 6
Chromosome location 6p21.1
Summary This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids
SNPs SNP information provided by dbSNP.
22
SNP ID Visualize variation Clinical significance Consequence
rs104893988 G>A Pathogenic Coding sequence variant, genic downstream transcript variant, stop gained
rs104893989 T>C,G Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
rs104893990 G>A Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
rs104893991 G>A Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
rs104893992 C>T Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
324
miRTarBase ID miRNA Experiments Reference
MIRT003597 hsa-miR-135b-5p qRT-PCR 19795981
MIRT004707 hsa-miR-155-5p Luciferase reporter assayqRT-PCRWestern blot 20427544
MIRT005888 hsa-miR-335-5p Luciferase reporter assayMicroarrayqRT-PCRWestern blot 21164520
MIRT006037 hsa-miR-203a-3p ImmunoblotIn situ hybridizationLuciferase reporter assayqRT-PCRWestern blot 21159887
MIRT006079 hsa-miR-497-5p Luciferase reporter assayNorthern blotqRT-PCRWestern blot 21350001
Transcription factors Transcription factors information provided by TRRUST V2 database.
10
Transcription factor Regulation Reference
CBFB Unknown 24648201
ESR1 Unknown 11604227
HDAC4 Repression 19509297
JUN Unknown 11604227
PITX1 Repression 21425961
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
92
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IEA
GO:0000785 Component Chromatin ISA
GO:0000785 Component Chromatin ISS
GO:0000976 Function Transcription cis-regulatory region binding IEA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
600211 10472 ENSG00000124813
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q13950
Protein name Runt-related transcription factor 2 (Acute myeloid leukemia 3 protein) (Core-binding factor subunit alpha-1) (CBF-alpha-1) (Oncogene AML-3) (Osteoblast-specific transcription factor 2) (OSF-2) (Polyomavirus enhancer-binding protein 2 alpha A subunit) (PEA
Protein function Transcription factor involved in osteoblastic differentiation and skeletal morphogenesis (PubMed:28505335, PubMed:28703881, PubMed:28738062). Essential for the maturation of osteoblasts and both intramembranous and endochondral ossification. CBF
PDB 6VG8 , 6VGD , 6VGE , 6VGG
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00853 Runt 102 231 Runt domain Domain
PF08504 RunxI 430 521 Runx inhibition domain Family
Tissue specificity TISSUE SPECIFICITY: Specifically expressed in osteoblasts.
Sequence
MASNSLFSTVTPCQQNFFWDPSTSRRFSPPSSSLQPGKMSDVSPVVAAQQQQQQQQQQQQ
QQQQQQQQQQQEAAAAAAAAAAAAAAAAAVPRLRPPHDNRTMVEIIADHPAELVRTDSPN
FLCSVLPSHWRCNKTLPVAFKVVALGEVPDGTVVTVMAGNDENYSAELRNASAVMKNQVA
RFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKVTVDGPREPRRHR
QKLDDSKPS
LFSDRLSDLGRIPHPSMRVGVPPQNPRPSLNSAPSPFNPQGQSQITDPRQAQSSPPWSYD
QSYPSYLSQMTSPSIHSTTPLSSTRGTGLPAITDVPRRISDDDTATSDFCLWPSTLSKKS
QAGASELGPFSDPRQFPSISSLTESRFSNPRMHYPATFTYTPPVTSGMSLGMSATTHYHT
YLPPPYPGSSQSQSGPFQTSSTPYLYYGTSSGSYQFPMVPGGDRSPSRMLPPCTTTSNGS
TLLNPNLPNQNDGVDADGSHSSSPTVLNSSGRMDESVWRPY
Sequence length 521
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Parathyroid hormone synthesis, secretion and action
Transcriptional misregulation in cancer
  Transcriptional regulation by RUNX2
RUNX1 regulates transcription of genes involved in differentiation of myeloid cells
Regulation of RUNX2 expression and activity
RUNX2 regulates osteoblast differentiation
RUNX2 regulates bone development
RUNX2 regulates genes involved in cell migration
RUNX2 regulates genes involved in differentiation of myeloid cells
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
44
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Cleidocranial dysostosis Pathogenic; Likely pathogenic rs2150368246, rs2150368229, rs2150452063, rs758120505, rs2150407600, rs2150368254, rs2150371825, rs2150362655, rs2150421218, rs2548589063, rs864621970, rs2481024368, rs730880313, rs104893988, rs104893989
View all (31 more)
RCV002499799
RCV001530973
RCV001823782
RCV001823783
RCV001823784
View all (42 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cleidocranial dysplasia 1, forme fruste, dental anomalies only Pathogenic rs104893993 RCV002293413
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cleidocranial dysplasia 1, forme fruste, with brachydactyly Pathogenic rs606231174 RCV002293411
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome Pathogenic; Likely pathogenic rs2150368246, rs1311296877, rs2150368254, rs104893991, rs1057521068, rs397515538 RCV002499799
RCV002286433
RCV006257350
RCV002482851
RCV005411429
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANDROGENETIC ALOPECIA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, PSORIATIC CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, RHEUMATOID CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acampomelic Campomelic Dysplasia Acampomelic Campomelic Dysplasia BEFREE 21890680
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 17312329
★☆☆☆☆
Found in Text Mining only
Acute myelomonocytic leukemia Myelomonocytic Leukemia BEFREE 23404246
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 1317749, 20368581, 28569789, 8309256
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 19915614, 27634876, 28631378, 31109257
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of large intestine Colorectal Cancer BEFREE 31059049
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 24677340
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 27706911
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 17312329
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 36764297 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations