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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
29
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
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)
Show/Hide Causal Diseases (4)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
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
View all (12 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cardiovascular phenotype Likely pathogenic; Pathogenic rs1409037310, rs2529843313, rs771708843, rs765464485 RCV005704898
RCV002403897
RCV002460012
RCV004524261
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ehlers-Danlos syndrome Pathogenic rs766853150 RCV002276571
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PRDM5-related disorder Pathogenic rs1409412200 RCV003966549
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Show/Hide Unknown Diseases (25)
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
AORTIC DISEASES — Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AORTIC DISORDER — GenCC
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (64)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenoma Adenoma BEFREE 23873026, 25613750
★★★★★
★☆☆☆☆
Found in Text Mining only
Anterior segment mesenchymal dysgenesis Anterior segment mesenchymal dysgenesis Pubtator 26489929 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Arachnodactyly Arachnodactyly HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Axenfeld-Rieger syndrome Axenfeld anomaly BEFREE 26489929
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Brittle cornea syndrome Brittle Cornea Syndrome Orphanet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Brittle cornea syndrome 1 Brittle cornea syndrome Pubtator 21664999, 23680354, 26395458, 26489929, 26560304 Associate
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BRITTLE CORNEA SYNDROME 2 Brittle Cornea Syndrome UNIPROT_DG 21664999
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
BRITTLE CORNEA SYNDROME 2 Brittle Cornea Syndrome GENOMICS_ENGLAND_DG 21664999, 22122778, 23680354
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
BRITTLE CORNEA SYNDROME 2 Brittle Cornea Syndrome BEFREE 26395458
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
BRITTLE CORNEA SYNDROME 2 Brittle Cornea Syndrome CLINVAR_DG
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)