PRDM5 (PR/SET domain 5)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID 11107
Gene name PR/SET domain 5
Gene symbol PRDM5
Synonyms (NCBI Gene)
BCS2PFM2
Chromosome 4
Chromosome location 4q27
Summary 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.
6
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.
6
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
33
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 identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
MIM HGNC e!Ensembl
614161 9349 ENSG00000138738
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
403
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide Causal Diseases (4)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Brittle cornea syndrome 2 Likely pathogenic; Pathogenic rs755802156, rs1734381962, rs2478057377, rs1409037310, rs1455476600, rs2477956523, rs755676779, rs2477547119, rs2477938090, rs2478065345, rs387907110, rs1267369024, rs387907111, rs766853150, rs1579259095
View all (2 more)		 RCV002223029
RCV002238653
RCV002282913
RCV003155475
RCV005028027
RCV003226833
RCV003389136
RCV005030144
RCV005030162
RCV005038551
RCV000024107
RCV000024108
RCV000024109
RCV000024110
RCV000024111
RCV001260236
RCV001260235
Cardiovascular phenotype Likely pathogenic; Pathogenic rs1409037310, rs2529843313, rs771708843, rs765464485 RCV005704898
RCV002403897
RCV002460012
RCV004524261
Ehlers-Danlos syndrome Pathogenic rs766853150 RCV002276571
PRDM5-related disorder Pathogenic rs1409412200 RCV003966549
Show/Hide Unknown Diseases (9)
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Axenfeld-Rieger syndrome type 1 Uncertain significance rs779601690 RCV000207198
Brittle cornea syndrome 1 Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity rs376740879, rs140634372, rs35363618, rs17051264, rs146228268, rs556802821, rs77157999, rs371617787, rs12499000, rs886059043, rs374500219, rs886059046, rs558723351, rs181244989, rs147796327
View all (14 more)		 RCV000395087
RCV000276233
RCV000307869
RCV000272520
RCV000280666
RCV000307248
RCV000340282
RCV000356841
RCV000312661
RCV000279273
RCV000349563
RCV000366631
RCV000271668
RCV000384381
RCV000286582
RCV000297279
RCV000325180
RCV000289939
RCV000341675
RCV000334286
RCV000398886
RCV000315336
RCV000377607
RCV000399185
RCV000268580
RCV000264339
RCV000375145
RCV000303367
RCV000358106
Cervical cancer Likely benign rs188427518 RCV005905466
Connective tissue disorder Conflicting classifications of pathogenicity rs199602365 RCV002278571
Show/Hide Text Mining Associations (28)
Associations from Text MiningDisease 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