U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 56980, updated on 11-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See PRDM10 in Genome Data Viewer
Location:
11q24.3
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (129899711..130002835, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (129935739..130038861, complement)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: 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

Go to the top of the pageHelp

Related articles in PubMed

  1. 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
  2. Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile. Hofvander J, et al. J Pathol, 2019 Dec. PMID 31313299
  3. Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma. Hofvander J, et al. Clin Cancer Res, 2015 Feb 15. PMID 25516889
  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. PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dubé syndrome and familial lipomatosis. van de Beek I, et al. Hum Mol Genet, 2023 Mar 20. PMID 36440963, Free PMC Article

See all (29) 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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

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

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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
part_of 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

Go to the top of the page Help
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
NP_001354819.1
NP_001354820.1
NP_001354821.1
NP_001354822.1
NP_001354823.1
NP_001354824.1
NP_001354825.1
NP_001354826.1
NP_001354827.1
NP_001354828.1
NP_064613.2
NP_955469.1
NP_955470.1
NP_955471.1
XP_011541214.1
XP_047283267.1
XP_047283268.1
XP_054225408.1
XP_054225409.1
XP_054225410.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_2023_10

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous