Gene Gene information from NCBI Gene database.
Entrez ID 7799
Gene name PR/SET domain 2
Gene symbol PRDM2
Synonyms (NCBI Gene)
HUMHOXY1KMT8KMT8AMTB-ZFRIZRIZ1RIZ2
Chromosome 1
Chromosome location 1p36.21
Summary This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 ge
SNPs SNP information provided by dbSNP.
1
SNP ID Visualize variation Clinical significance Consequence
rs1570018597 TAGTACAGAAAGC>- Likely-pathogenic Intron variant, non coding transcript variant, frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
392
miRTarBase ID miRNA Experiments Reference
MIRT038603 hsa-miR-106b-3p CLASH 23622248
MIRT626956 hsa-miR-548c-3p HITS-CLIP 23824327
MIRT626955 hsa-miR-4668-3p HITS-CLIP 23824327
MIRT626954 hsa-miR-605-5p HITS-CLIP 23824327
MIRT626953 hsa-miR-188-5p HITS-CLIP 23824327
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
YY1 Activation 18488713
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
29
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 9334209
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP 8654390
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
GO:0001227 Function DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 9334209
GO:0001228 Function DNA-binding transcription activator activity, RNA polymerase II-specific IDA 8654390
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
601196 9347 ENSG00000116731
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q13029
Protein name PR domain zinc finger protein 2 (EC 2.1.1.355) (GATA-3-binding protein G3B) (Lysine N-methyltransferase 8) (MTB-ZF) (MTE-binding protein) (PR domain-containing protein 2) (Retinoblastoma protein-interacting zinc finger protein) (Zinc finger protein RIZ)
Protein function S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme
PDB 2JV0 , 2QPW
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00856 SET 41 141 SET domain Family
PF00096 zf-C2H2 360 382 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 390 412 Zinc finger, C2H2 type Domain
PF13912 zf-C2H2_6 482 508 Domain
PF13912 zf-C2H2_6 1454 1475 Domain
Tissue specificity TISSUE SPECIFICITY: Highly expressed in retinoblastoma cell lines and in brain tumors. Also expressed in a number of other cell lines and in brain, heart, skeletal muscle, liver and spleen. Isoform 1 is expressed in testis at much higher level than isofor
Sequence
MNQNTTEPVAATETLAEVPEHVLRGLPEEVRLFPSAVDKTRIGVWATKPILKGKKFGPFV
GDKKKRSQVKNNVYMWEVYYPNLGWMCIDATDPEKGNWLRYVNWACSGEEQNLFPLEINR
AIYYKTLKPIAPGEELLVWYN
GEDNPEIAAAIEEERASARSKRSSPKSRKGKKKSQENKN
KGNKIQDIQLKTSEPDFTSANMRDSAEGPKEDEEKPSASALEQPATLQEVASQEVPPELA
TPAPAWEPQPEPDERLEAAACEVNDLGEEEEEEEEEDEEEEEDDDDDELEDEGEEEASMP
NENSVKEPEIRCDEKPEDLLEEPKTTSEETLEDCSEVTPAMQIPRTKEEANGDVFETFMF
PCQHCERKFTTKQGLERHMHIH
ISTVNHAFKCKYCGKAFGTQINRRRHERRHEAGLKRKP
SQTLQPSEDLADGKASGENVASKDDSSPPSLGPDCLIMNSEKASQDTINSSVVEENGEVK
ELHPCKYCKKVFGTHTNMRRHQRRVHERHLIPKGVRRKGGLEEPQPPAEQAQATQNVYVP
STEPEEEGEADDVYIMDISSNISENLNYYIDGKIQTNNNTSNCDVIEMESASADLYGINC
LLTPVTVEITQNIKTTQVPVTEDLPKEPLGSTNSEAKKRRTASPPALPKIKAETDSDPMV
PSCSLSLPLSISTTEAVSFHKEKSVYLSSKLKQLLQTQDKLTPAGISATEIAKLGPVCVS
APASMLPVTSSRFKRRTSSPPSSPQHSPALRDFGKPSDGKAAWTDAGLTSKKSKLESHSD
SPAWSLSGRDERETVSPPCFDEYKMSKEWTASSAFSSVCNQQPLDLSSGVKQKAEGTGKT
PVQWESVLDLSVHKKHCSDSEGKEFKESHSVQPTCSAVKKRKPTTCMLQKVLLNEYNGID
LPVENPADGTRSPSPCKSLEAQPDPDLGPGSGFPAPTVESTPDVCPSSPALQTPSLSSGQ
LPPLLIPTDPSSPPPCPPVLTVATPPPPLLPTVPLPAPSSSASPHPCPSPLSNATAQSPL
PILSPTVSPSPSPIPPVEPLMSAASPGPPTLSSSSSSSSSSSSFSSSSSSSSPSPPPLSA
ISSVVSSGDNLEASLPMISFKQEELENEGLKPREEPQSAAEQDVVVQETFNKNFVCNVCE
SPFLSIKDLTKHLSIHAEEWPFKCEFCVQLFKDKTDLSEHRFLLHGVGNIFVCSVCKKEF
AFLCNLQQHQRDLHPDKVCTHHEFESGTLRPQNFTDPSKAHVEHMQSLPEDPLETSKEEE
ELNDSSEELYTTIKIMASGIKTKDPDVRLGLNQHYPSFKPPPFQYHHRNPMGIGVTATNF
TTHNIPQTFTTAIRCTKCGKGVDNMPELHKHILACASASDKKRYTPKKNPVPLKQTVQPK
NGVVVLDNSGKNAFRRMGQPKRLNFSVELSKMSSNKLKLNALKKKNQLVQKAILQKNKSA
KQKADLKNACESSSHICPYCNREFTYIGSLNKHAAFSCPKKPLSPPKKKVSHSSKKGGHS
SPASSDKNSNSNHRRRTADAEIKMQSMQTPLGKTRARSSGPTQVPLPSSSFRSKQNVKFA
ASVKSKKPSSSSLRNSSPIRMAKITHVEGKKPKAVAKNHSAQLSSKTSRSLHVRVQKSKA
VLQSKSTLASKKRTDRFNIKSRERSGGPVTRSLQLAAAADLSENKREDGSAKQELKDFSY
SLRLASRCSPPAAPYITRQYRKVKAPAAAQFQGPFFKE
Sequence length 1718
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Lysine degradation
Metabolic pathways
 
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
9
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
Flexion contracture Likely pathogenic rs1570018597 RCV001007819
★★★★☆
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
AMPHETAMINE OR RELATED ACTING SYMPATHOMIMETIC ABUSE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AMPHETAMINE-RELATED DISORDERS CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BRAIN ANEURYSM GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Low bone mineral density Benign ClinVar
★★☆☆☆
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
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 12472571
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 17693662
★☆☆☆☆
Found in Text Mining only
Adrenal Gland Pheochromocytoma Adrenal Gland Pheochromocytoma BEFREE 14668725, 15809732
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 22300346
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 14688019
★☆☆☆☆
Found in Text Mining only
Benign Meningioma Benign Meningioma BEFREE 22614009
★☆☆☆☆
Found in Text Mining only
Benign Neoplasm Benign Neoplasm BEFREE 17103461
★☆☆☆☆
Found in Text Mining only
Bladder Neoplasm Bladder Neoplasm CTD_human_DG 26039340
★☆☆☆☆
Found in Text Mining only
Blast Phase Blast phase chronic myelogenous leukemia BEFREE 16953217, 18246120, 19602237
★☆☆☆☆
Found in Text Mining only
Brain Neoplasms Brain neoplasms Pubtator 8654390 Associate
★☆☆☆☆
Found in Text Mining only