PHF10 PHD finger protein 10 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHF10provided by HGNC
Official Full Name: PHD finger protein 10provided by HGNC
Primary source: HGNC:HGNC:18250
See related: Ensembl:ENSG00000130024 MIM:613069; AllianceGenome:HGNC:18250
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: BAF45A; XAP135; SMARCG4
Summary: This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known. Sequence analysis suggests that multiple alternatively spliced transcript variants are derived from this gene but the full-length nature of only two of them is known. These two splice variants encode different isoforms. A pseudogene for this gene is located on Xq28. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in adrenal (RPKM 31.1), ovary (RPKM 25.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q27

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (169703902..169724500, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (171057816..171078422, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (170103998..170124596, complement)

Chromosome 6 - NC_000006.12 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?

Neuronal and Muscle Differentiation of Mammalian Cells Is Accompanied by a Change in PHF10 Isoform Expression.
Title: Neuronal and Muscle Differentiation of Mammalian Cells Is Accompanied by a Change in PHF10 Isoform Expression.
ZC3H13-mediated N6-methyladenosine modification of PHF10 is impaired by fisetin which inhibits the DNA damage response in pancreatic cancer.
Title: ZC3H13-mediated N6-methyladenosine modification of PHF10 is impaired by fisetin which inhibits the DNA damage response in pancreatic cancer.
PHF10 subunit of PBAF complex mediates transcriptional activation by MYC.
Title: PHF10 subunit of PBAF complex mediates transcriptional activation by MYC.
The sequential phosphorylation of PHF10 subunit of the PBAF chromatin-remodeling complex determines different properties of the PHF10 isoforms.
Title: The sequential phosphorylation of PHF10 subunit of the PBAF chromatin-remodeling complex determines different properties of the PHF10 isoforms.
PHF10 expression in cells of different lines is activated by the c-MYC oncogene. Since PHF10 stimulates cell proliferation, its c-MYC-dependent activation in cancer cells should lead to an increase in their proliferation rate.
Title: Oncogene c-MYC Controls the Expression of PHF10 Subunit of PBAF Chromatin Remodeling Complex in SW620 Cell Line.
Data show that PHF10 subunit of the PBAF signature module is the most unstable PBAF subunit, and demonstrate an important role of beta-TrCP ubiquitin ligase in regulation of PHF10 level and PBAF in general. Also, PHF10 isoforms contained two non-canonical beta-TrCP degrons and are degraded by beta-TrCP in a phospho-dependent manner.
Title: Stability of the PHF10 subunit of PBAF signature module is regulated by phosphorylation: role of β-TrCP.
We studied the expression of S100A4 and the total PHF10 protein in some human cancer cell lines. We have found that, in the cell lines studied, the PHF10 expression is correlated with the S100A4 expression.
Title: The level of the Phf10 protein, a PBAF chromatin-remodeling complex subunit, correlates with the Mts1/S100A4 expression in human cancer cell lines.
Phosphorylation of PHF10 isoforms occurs while they are incorporated as a subunit of the PBAF complex, and therefore phosphorylation of PHF10 isoforms may play an essential role in regulation of PBAF complex's function and mechanism of action.
Title: [PHF10 isoforms are phosphorylated in the PBAF mammalian chromatin remodeling complex].
The study demonstrates the existence of functionally different PBAF complexes in mammalian cell. It also provides an insight into the molecular structure and role of human PHF10/BAF45a and characterizes it as an essential PBAF subunit.
Title: Mammalian cells contain two functionally distinct PBAF complexes incorporating different isoforms of PHF10 signature subunit.
PHF10 repressed caspase-3 expression and impaired the programmed cell death pathway in human gastric cancer at the transcriptional level.
Title: A novel plant homeodomain finger 10-mediated antiapoptotic mechanism involving repression of caspase-3 in gastric cancer cells.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1237E (e-PCR)
- UniSTS:39174

RH93665 (e-PCR)
- UniSTS:88865

RH35932 (e-PCR)
- UniSTS:51033

RH36593 (e-PCR)
- UniSTS:47464

G19729 (e-PCR)
- UniSTS:33673

A001W43 (e-PCR)
- UniSTS:33674

D6S1902 (e-PCR)
- UniSTS:9681

D6S1117E (e-PCR)
- UniSTS:11481

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone acetyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of double-strand break repair	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of myoblast differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of G0 to G1 transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of G1/S transition of mitotic cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of mitotic metaphase/anaphase transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of nucleotide-excision repair	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of RSC-type complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	NAS Non-traceable Author Statement more info	PubMed
located_in kinetochore	NAS Non-traceable Author Statement more info	PubMed
part_of npBAF complex	ISS Inferred from Sequence or Structural Similarity more info
part_of npBAF complex	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: PHD finger protein 10

Names: BRG1-associated factor 45a; BRG1-associated factor, 45-KD, A; PHD zinc finger protein XAP135

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_018288.4 → NP_060758.2 PHD finger protein 10 isoform a

See identical proteins and their annotated locations for NP_060758.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform.

Source sequence(s)

AL513547, BC110323, DB460742

Consensus CDS

CCDS5308.2

UniProtKB/Swiss-Prot

Q2YDA3, Q53HG8, Q8WUB8, Q9BXD2, Q9NV26

UniProtKB/TrEMBL

S5FMB0

Related

ENSP00000341805.4, ENST00000339209.9

Conserved Domains (3) summary

cd15528
Location:379 → 433

PHD1_PHF10; PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins

cd15529
Location:435 → 478

PHD2_PHF10; PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins

cd21085
Location:73 → 161

WH_NTD_PHF10; N-terminal winged helix DNA-binding domain found in PHD finger protein 10 (PHF10) and similar proteins
NM_133325.3 → NP_579866.2 PHD finger protein 10 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice junction which results in 6 fewer nt when compared to variant 1. It encodes an isoform (b) that lacks 2 internal amino acids compared to isoform a.

Source sequence(s)

AL513547

Consensus CDS

CCDS5309.2

UniProtKB/TrEMBL

S5FMB0

Related

ENSP00000355743.4, ENST00000366780.8

Conserved Domains (2) summary

cd15528
Location:377 → 431

PHD1_PHF10; PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins

cd15529
Location:433 → 476

PHD2_PHF10; PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins