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

Summary

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

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes.
Title: Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes.
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.
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.
PRDM10-fusions represent the critical driver mutations in undifferentiated pleomorphic sarcomas.
Title: Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile.
Our results suggest that PRDM10 fusions are present in around 5% of Undifferentiated pleomorphic sarcoma
Title: Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.

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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)

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

D11S4274 (e-PCR)
- UniSTS:41739

RH70351 (e-PCR)
- UniSTS:70961

G20316 (e-PCR)
- UniSTS:24901

A005L34 (e-PCR)
- UniSTS:24902

SHGC-108125 (e-PCR)
- UniSTS:182354

GDB:181268 (e-PCR)
- UniSTS:155229

D11S2281E (e-PCR)
- UniSTS:24718

D11S4283 (e-PCR)
- UniSTS:33466

D11S1199 (e-PCR)
- UniSTS:55762

D11S3991 (e-PCR)
- UniSTS:81399

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

NP_001354819.1

EC 2.1.1.-

NP_001354820.1

EC 2.1.1.-

NP_001354821.1

EC 2.1.1.-

NP_001354822.1

EC 2.1.1.-

NP_001354823.1

EC 2.1.1.-

NP_001354824.1

EC 2.1.1.-

NP_001354825.1

EC 2.1.1.-

NP_001354826.1

EC 2.1.1.-

NP_001354827.1

EC 2.1.1.-

NP_001354828.1

EC 2.1.1.-

NP_064613.2

EC 2.1.1.-

NP_955469.1

EC 2.1.1.-

NP_955470.1

EC 2.1.1.-

NP_955471.1

EC 2.1.1.-

XP_011541214.1

EC 2.1.1.-

XP_047283267.1

EC 2.1.1.-

XP_047283268.1

EC 2.1.1.-

XP_054225408.1

EC 2.1.1.-

XP_054225409.1

EC 2.1.1.-

XP_054225410.1

EC 2.1.1.-

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)

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

Status: REVIEWED

Source sequence(s)

AP003326, AP003327

UniProtKB/TrEMBL

B7ZL72
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
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
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
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
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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

129899711..130002835 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A2Z2E6H7
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
XM_047427311.1 → XP_047283267.1 PR domain zinc finger protein 10 isoform X2

UniProtKB/TrEMBL

A0A2Z2E6H7

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

129935739..130038861 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A2Z2E6H7
XM_054369433.1 → XP_054225408.1 PR domain zinc finger protein 10 isoform X1

UniProtKB/TrEMBL

A0A2Z2E6H7
XM_054369434.1 → XP_054225409.1 PR domain zinc finger protein 10 isoform X2

UniProtKB/TrEMBL

A0A2Z2E6H7