PRDM5 (PR/SET domain 5)

Gene
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
11107
Gene name Gene Name - the full gene name approved by the HGNC.
PR/SET domain 5
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
PRDM5
Synonyms (NCBI Gene) Gene synonyms aliases
BCS2, PFM2
Chromosome Chromosome number
4
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
4q27
Summary Summary of gene provided in NCBI Entrez Gene.
The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorig
SNPs SNP information provided by dbSNP.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all(6)
SNP ID Visualize variation Clinical significance Consequence
rs185134294 G>A Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance Genic downstream transcript variant, intron variant
rs387907110 G>A,T Pathogenic Stop gained, intron variant, coding sequence variant, synonymous variant, 3 prime UTR variant, genic downstream transcript variant
rs387907111 T>A,C Pathogenic Coding sequence variant, genic upstream transcript variant, non coding transcript variant, 5 prime UTR variant, missense variant
rs766853150 C>- Pathogenic 5 prime UTR variant, coding sequence variant, non coding transcript variant, frameshift variant
rs1057517804 ->C Likely-pathogenic Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
miRNA miRNA information provided by mirtarbase database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all(6)
miRTarBase ID miRNA Experiments Reference
MIRT494928 hsa-miR-8063 PAR-CLIP 23708386
MIRT494928 hsa-miR-8063 PAR-CLIP 23708386
MIRT1260320 hsa-miR-136 CLIP-seq
MIRT1260321 hsa-miR-3617 CLIP-seq
MIRT1260322 hsa-miR-515-5p CLIP-seq
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all(33)
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 17636019
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IMP 21664999
GO:0000278 Process Mitotic cell cycle IMP 17636019
GO:0000976 Function Transcription cis-regulatory region binding IDA 17636019
GO:0000976 Function Transcription cis-regulatory region binding IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
MIM HGNC e!Ensembl
614161 9349 ENSG00000138738
Protein
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
UniProt ID Q9NQX1
Protein name PR domain zinc finger protein 5 (EC 2.1.1.-) (PR domain-containing protein 5)
Protein function Sequence-specific DNA-binding transcription factor. Represses transcription at least in part by recruitment of the histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1. Regulates hematopoiesis-associated protein-coding and
PDB 6XAZ
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00096 zf-C2H2 199 → 220 Zinc finger, C2H2 type Domain
PF12874 zf-met 234 → 254 Domain
PF12874 zf-met 295 → 317 Domain
PF00096 zf-C2H2 320 → 342 Zinc finger, C2H2 type Domain
PF13912 zf-C2H2_6 348 → 372 Domain
PF12874 zf-met 376 → 398 Domain
PF00096 zf-C2H2 404 → 426 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 432 → 455 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 461 → 483 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 490 → 511 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 517 → 539 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 545 → 567 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 573 → 595 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 603 → 625 Zinc finger, C2H2 type Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed with highest levels in colon and ovary. Tends to be silenced in breast, colorectal, gastric and liver cancer tissues. {ECO:0000269|PubMed:15077163, ECO:0000269|PubMed:17699856}.
Sequence 
MLGMYVPDRFSLKSSRVQDGMGLYTARRVRKGEKFGPFAGEKRMPEDLDENMDYRLMWEV
RGSKGEVLYILDATNPRHSNWLRFVHEAPSQEQKNLAAIQEGENIFYLAVEDIETDTELL
IGYLDSDMEAEEEEQQIMTVIKEGEVENSRRQSTAGRKDRLGCKEDYACPQCESSFTSED
ILAEHLQTLHQKPTEEKEFKCKNCGKKFPVKQALQRHVLQCTAKSSLKESSRSFQCSVCN
SSFSSASSFEQHQETCRGDARFVCKADSCGKRLKSKDALKRHQENVHTGDPKKKLICSVC
NKKCSSASSLQEHRKIHEIFDCQECMKKFISANQLKRHMITHSEKRPYNCEICNKSFKRL
DQVGAHKVIHSEDKPYKCKLCGKGFAHRNVYKNHKKTHSEERPFQCEECKALFRTPFSLQ
RHLLIHNSERTFKCHHCDATFKRKDTLNVHVQVVHERHKKYRCELCNKAFVTPSVLRSHK
KTHTGEKEKICPYCGQKFASSGTLRVHIRSHTGERPYQCPYCEKGFSKNDGLKMHIRTHT
REKPYKCSECSKAFSQKRGLDEHKRTHTGEKPFQCDVCDLAFSLKKMLIRHKMTHNPNRP
LAECQFCHKKFTRNDYLKVHMDNIHGVADS
Sequence length 630
Interactions View interactions
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide Causal Diseases (2)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Brittle Cornea Syndrome brittle cornea syndrome 2 rs387907110, rs1267369024, rs387907111, rs766853150, rs1579259095 N/A
Ehlers-Danlos Syndrome ehlers-danlos syndrome rs766853150 N/A
Show/Hide Unknown Diseases (3)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Axenfeld anomaly Axenfeld-Rieger syndrome type 1, Axenfeld-Rieger syndrome N/A N/A ClinVar, GenCC
Connective Tissue Disease Connective tissue disorder N/A N/A ClinVar
Diabetes Type 2 diabetes N/A N/A GWAS
Show/Hide Text Mining Associations (28)
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Abnormalities Drug Induced Associate 26560304
Adenocarcinoma of Lung Associate 36127737
Anterior segment mesenchymal dysgenesis Associate 26489929
Axenfeld Rieger syndrome Associate 26489929
Basal Laminar Drusen Associate 26560304
Brittle cornea syndrome 1 Associate 21664999, 23680354, 26395458, 26489929, 26560304
Carcinogenesis Associate 20213097
Choroidal Neovascularization Associate 26560304
Colorectal Neoplasms Associate 25613750
Corneal Diseases Associate 21664999