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    PRDM10 PR/SET domain 10 [ Homo sapiens (human) ]

    Gene ID: 56980, updated on 30-Oct-2024

    Summary

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    Official Symbol
    PRDM10provided by HGNC
    Official Full Name
    PR/SET domain 10provided by HGNC
    Primary source
    HGNC:HGNC:13995
    See related
    Ensembl:ENSG00000170325 MIM:618319; AllianceGenome:HGNC:13995
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BHD2; PFM7; TRIS
    Summary
    The protein encoded by this gene is a transcription factor that contains C2H2-type zinc-fingers. It also contains a positive regulatory domain, which has been found in several other zinc-finger transcription factors including those involved in B cell differentiation and tumor suppression. Studies of the mouse counterpart suggest that this protein may be involved in the development of the central nerve system (CNS), as well as in the pathogenesis of neuronal storage disease. Multiple alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 1.6), lymph node (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRDM10 in Genome Data Viewer
    Location:
    11q24.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (129899711..130002835, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (129935739..130038861, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (129769606..129872730, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 45B Neighboring gene TMEM45B-NFRKB intergenic CAGE-defined mid-level expression enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr11:129739277-129739466 Neighboring gene Sharpr-MPRA regulatory region 15352 Neighboring gene nuclear factor related to kappaB binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4068 Neighboring gene NANOG hESC enhancer GRCh37_chr11:129795831-129796332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:129806281-129806994 Neighboring gene MPRA-validated peak1509 silencer Neighboring gene Sharpr-MPRA regulatory region 3666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:129841453-129842000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4073 Neighboring gene CRISPRi-validated cis-regulatory element chr11.6035 Neighboring gene PRDM10 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4074 Neighboring gene Sharpr-MPRA regulatory region 13105 Neighboring gene NANOG hESC enhancer GRCh37_chr11:129907707-129908249 Neighboring gene MPRA-validated peak1512 silencer Neighboring gene elongin B pseudogene 2 Neighboring gene uncharacterized LOC107984432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:129938480-129938980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:129938981-129939481

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes. Li L, et al. Biochem Biophys Res Commun, 2023 Oct 15. PMID 37566921
    2. PRDM10 RCC: A Birt-Hogg-Dubé-like Syndrome Associated With Lipoma and Highly Penetrant, Aggressive Renal Tumors Morphologically Resembling Type 2 Papillary Renal Cell Carcinoma. Schmidt LS, et al. Urology, 2023 Sep. PMID 37331486, Free PMC Article
    3. Recurrent PRDM10 Fusions in Superficial CD34-Positive Fibroblastic Tumors : A Clinicopathologic and Molecular Study of 10 Additional Cases of an Emerging Novel Entity. Zhao M, et al. Am J Clin Pathol, 2023 Apr 4. PMID 36812381
    4. Ectopic dendrite initiation: CNS pathogenesis as a model of CNS development. Siegel DA, et al. Int J Dev Neurosci, 2002 Jun-Aug. PMID 12175877
    5. Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma. Hofvander J, et al. Clin Cancer Res, 2015 Feb 15. PMID 25516889

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRDM10 RCC: A Birt-Hogg-Dube-like Syndrome Associated With Lipoma and Highly Penetrant, Aggressive Renal Tumors Morphologically Resembling Type 2 Papillary Renal Cell Carcinoma.
      Title: PRDM10 RCC: A Birt-Hogg-Dubé-like Syndrome Associated With Lipoma and Highly Penetrant, Aggressive Renal Tumors Morphologically Resembling Type 2 Papillary Renal Cell Carcinoma.
    2. Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes.
      Title: Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes.
    3. Recurrent PRDM10 Fusions in Superficial CD34-Positive Fibroblastic Tumors : A Clinicopathologic and Molecular Study of 10 Additional Cases of an Emerging Novel Entity.
      Title: Recurrent PRDM10 Fusions in Superficial CD34-Positive Fibroblastic Tumors : A Clinicopathologic and Molecular Study of 10 Additional Cases of an Emerging Novel Entity.
    4. PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dube syndrome and familial lipomatosis.
      Title: PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dubé syndrome and familial lipomatosis.
    5. PRDM10-fusions represent the critical driver mutations in undifferentiated pleomorphic sarcomas.
      Title: Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile.
    6. Our results suggest that PRDM10 fusions are present in around 5% of Undifferentiated pleomorphic sarcoma
      Title: Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma.
    7. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Novel breast cancer risk alleles and interaction with ionizing radiation among U.S. radiologic technologists.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Birt-Hogg-Dube syndrome 2
    MedGen: C5830676 OMIM: 620459 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of PR domain containing 10 (PRDM10) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed
    Knockdown of PR domain containing 10 (PRDM10) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1231, MGC131802

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of transcription repressor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PR domain zinc finger protein 10
    Names
    PR domain 10
    PR domain containing 10
    PR domain-containing protein 10
    PR-domain family member 7
    PRDM zinc finger transcription factor
    tristanin

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001367890.1 → NP_001354819.1  PR domain zinc finger protein 10 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      A0A2Z2E6H7

    2. NM_001367891.1 → NP_001354820.1  PR domain zinc finger protein 10 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      A0A2Z2E6H7

    3. NM_001367892.1 → NP_001354821.1  PR domain zinc finger protein 10 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      A0A2Z2E6H7

    4. NM_001367893.1 → NP_001354822.1  PR domain zinc finger protein 10 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/Swiss-Prot
      B7ZL71, G3XAE5, J3KP23, Q17R90, Q2KHR4, Q863Z2, Q9NQV6, Q9NXI4, Q9ULI9
      UniProtKB/TrEMBL
      A0A2Z2E6H7

    5. NM_001367894.1 → NP_001354823.1  PR domain zinc finger protein 10 isoform 11

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      A0A2Z2E6H7

    6. NM_001367895.1 → NP_001354824.1  PR domain zinc finger protein 10 isoform 14

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      B7ZL72

    7. NM_001367896.1 → NP_001354825.1  PR domain zinc finger protein 10 isoform 13

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      B7ZL72

    8. NM_001367897.1 → NP_001354826.1  PR domain zinc finger protein 10 isoform 12

      Status: REVIEWED

      Source sequence(s)
      AP003041, AP003326, AP003327
      UniProtKB/TrEMBL
      B7ZL72

    9. NM_001367898.1 → NP_001354827.1  PR domain zinc finger protein 10 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AP003326, AP003327
      UniProtKB/TrEMBL
      B7ZL72

    10. NM_001367899.1 → NP_001354828.1  PR domain zinc finger protein 10 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AP003326, AP003327, BC143612
      Consensus CDS
      CCDS91624.1
      UniProtKB/TrEMBL
      B7ZL72
      Related
      ENSP00000432237.1, ENST00000526082.5

    11. NM_020228.3 → NP_064613.2  PR domain zinc finger protein 10 isoform 1

      See identical proteins and their annotated locations for NP_064613.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AP003041, AP003326, AP003327
      Consensus CDS
      CCDS44771.1
      UniProtKB/TrEMBL
      A0A2Z2E6H7
      Related
      ENSP00000351686.5, ENST00000358825.9
      Conserved Domains (5) summary
      COG5048
      Location:559 → 692
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:618 → 638
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:644 → 666
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:220 → 325
      SET; SET domain
      pfam16638
      Location:405 → 510
      Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers

    12. NM_199437.2 → NP_955469.1  PR domain zinc finger protein 10 isoform 2

      See identical proteins and their annotated locations for NP_955469.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. The resulting isoform (2) lacks an internal region, as compared to isoform 1.
      Source sequence(s)
      AP003041, AP003326, AP003327
      Consensus CDS
      CCDS8484.1
      UniProtKB/TrEMBL
      A0A2Z2E6H7
      Related
      ENSP00000354118.3, ENST00000360871.8
      Conserved Domains (5) summary
      COG5048
      Location:555 → 688
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:614 → 634
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:640 → 662
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:220 → 325
      SET; SET domain
      pfam16638
      Location:405 → 510
      Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers

    13. NM_199438.2 → NP_955470.1  PR domain zinc finger protein 10 isoform 3

      See identical proteins and their annotated locations for NP_955470.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences compared to the variant 1. The resulting isoform (3) has a distinct and shorter N-terminus, and lacks an internal region, as compared to isoform 1.
      Source sequence(s)
      AP003326, AP003327
      Consensus CDS
      CCDS44772.1
      UniProtKB/TrEMBL
      B7ZL72
      Related
      ENSP00000398431.2, ENST00000423662.6
      Conserved Domains (4) summary
      sd00017
      Location:532 → 552
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:558 → 580
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:134 → 239
      SET; SET domain
      pfam16638
      Location:319 → 424
      Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers

    14. NM_199439.2 → NP_955471.1  PR domain zinc finger protein 10 isoform 4

      See identical proteins and their annotated locations for NP_955471.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences compared to variant 1. The resulting isoform (4) has a distinct and shorter N-terminus and lacks two internal regions, as compared to isoform 1.
      Source sequence(s)
      AP003326, AP003327
      Consensus CDS
      CCDS8485.1
      UniProtKB/TrEMBL
      B7ZL72
      Related
      ENSP00000302669.6, ENST00000304538.10
      Conserved Domains (4) summary
      sd00017
      Location:528 → 548
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:554 → 576
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:134 → 239
      SET; SET domain
      pfam16638
      Location:319 → 424
      Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      129899711..130002835 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427312.1 → XP_047283268.1  PR domain zinc finger protein 10 isoform X3

    2. XM_011542912.3 → XP_011541214.1  PR domain zinc finger protein 10 isoform X1

      UniProtKB/TrEMBL
      A0A2Z2E6H7
      Related
      ENSP00000431262.1, ENST00000528746.5
      Conserved Domains (4) summary
      sd00017
      Location:614 → 634
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:640 → 662
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:220 → 325
      SET; SET domain
      pfam16638
      Location:405 → 510
      Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers

    3. XM_047427311.1 → XP_047283267.1  PR domain zinc finger protein 10 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      129935739..130038861 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369435.1 → XP_054225410.1  PR domain zinc finger protein 10 isoform X3

    2. XM_054369433.1 → XP_054225408.1  PR domain zinc finger protein 10 isoform X1

    3. XM_054369434.1 → XP_054225409.1  PR domain zinc finger protein 10 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQV6.3 GenPept UniProtKB/Swiss-Prot:Q9NQV6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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