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PHF6 PHD finger protein 6 [ Homo sapiens (human) ]

Gene ID: 84295, updated on 3-Nov-2024

Summary

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Official Symbol
PHF6provided by HGNC
Official Full Name
PHD finger protein 6provided by HGNC
Primary source
HGNC:HGNC:18145
See related
Ensembl:ENSG00000156531 MIM:300414; AllianceGenome:HGNC:18145
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
BFLS; BORJ; CENP-31
Summary
This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by cognitive disability, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in ovary (RPKM 17.4), lymph node (RPKM 13.6) and 25 other tissues See more
Orthologs
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Genomic context

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See PHF6 in Genome Data Viewer
Location:
Xq26.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (134373312..134428790)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (132698463..132753940)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (133507342..133562820)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chrX:133374068-133374687 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:133381318-133381517 Neighboring gene coiled-coil domain containing 160 Neighboring gene NT5DC1 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:133515535-133515735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21008 Neighboring gene origin of replication in promoter/intron 1 of HPRT1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21009 Neighboring gene hypoxanthine phosphoribosyltransferase 1 Neighboring gene ribosomal protein L36a pseudogene 54

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression.
    Title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression.
  2. Investigating the physiological role of S199A and S199D mutants of PHF6 protein in T-cell acute lymphoblastic leukemia.
    Title: Investigating the physiological role of S199A and S199D mutants of PHF6 protein in T-cell acute lymphoblastic leukemia.
  3. Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting.
    Title: Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting.
  4. PHF6 recruits BPTF to promote HIF-dependent pathway and progression in YAP-high breast cancer.
    Title: PHF6 recruits BPTF to promote HIF-dependent pathway and progression in YAP-high breast cancer.
  5. PHF6 promotes the progression of endometrial carcinoma by increasing cancer cells growth and decreasing T-cell infiltration.
    Title: PHF6 promotes the progression of endometrial carcinoma by increasing cancer cells growth and decreasing T-cell infiltration.
  6. PHF6 mutation is associated with poor outcome in acute myeloid leukaemia.
    Title: PHF6 mutation is associated with poor outcome in acute myeloid leukaemia.
  7. The Role of PHF6 in Hematopoiesis and Hematologic Malignancies.
    Title: The Role of PHF6 in Hematopoiesis and Hematologic Malignancies.
  8. MiR-1306-5p promotes cell proliferation and inhibits cell apoptosis in acute myeloid leukemia by downregulating PHF6 expression.
    Title: MiR-1306-5p promotes cell proliferation and inhibits cell apoptosis in acute myeloid leukemia by downregulating PHF6 expression.
  9. Further characterization of Borjeson-Forssman-Lehmann syndrome in females due to de novo variants in PHF6.
    Title: Further characterization of Borjeson-Forssman-Lehmann syndrome in females due to de novo variants in PHF6.
  10. Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair.
    Title: Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair.
Submit: New GeneRIF Correction See all GeneRIFs (55)

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
Borjeson-Forssman-Lehmann syndrome
MedGen: C0265339 OMIM: 301900 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-24)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2021-02-24)

ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC14797

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables histone deacetylase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone deacetylase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphoprotein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribonucleoprotein complex binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables scaffold protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tubulin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in blastocyst hatching IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in kinetochore IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
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 6
Names
PHD-like zinc finger protein
centromere protein 31

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.

Genomic

  1. NG_008886.1 RefSeqGene

    Range
    5001..60481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_629

mRNA and Protein(s)

  1. NM_001015877.2 → NP_001015877.1  PHD finger protein 6 isoform 1

    See identical proteins and their annotated locations for NP_001015877.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also called the "PHF6a" variant) represents the shortest transcript and encodes the shortest isoform (1).
    Source sequence(s)
    AB058726, AW297001, AY157622, BG122271, CF242973
    Consensus CDS
    CCDS14639.1
    UniProtKB/Swiss-Prot
    A8K230, B4E0G4, D3DTG3, E9PC97, Q5JRC7, Q5JRC8, Q8IWS0, Q96JK3, Q9BRU0
    UniProtKB/TrEMBL
    Q5JRC6
    Related
    ENSP00000359839.4, ENST00000370803.8
    Conserved Domains (2) summary
    cd15710
    Location:17 → 131
    ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
    cd15711
    Location:212 → 329
    ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)

  2. NM_032335.3 → NP_115711.2  PHD finger protein 6 isoform 2

    See identical proteins and their annotated locations for NP_115711.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate termination site, resulting in a distinct C-terminus (isoform 2).
    Source sequence(s)
    AK290095, BC005994, DR000282
    Consensus CDS
    CCDS14640.1
    UniProtKB/TrEMBL
    Q5JRC6
    Related
    ENSP00000359836.4, ENST00000370800.4
    Conserved Domains (2) summary
    cd15710
    Location:17 → 131
    ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
    cl22851
    Location:213 → 283
    PHD_SF; PHD finger superfamily

  3. NM_032458.3 → NP_115834.1  PHD finger protein 6 isoform 1

    See identical proteins and their annotated locations for NP_115834.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also called the 'PHF6b' variant) differs in the 3' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB058726, AW297001, AY157622, BG122271
    Consensus CDS
    CCDS14639.1
    UniProtKB/Swiss-Prot
    A8K230, B4E0G4, D3DTG3, E9PC97, Q5JRC7, Q5JRC8, Q8IWS0, Q96JK3, Q9BRU0
    UniProtKB/TrEMBL
    Q5JRC6
    Related
    ENSP00000329097.3, ENST00000332070.7
    Conserved Domains (2) summary
    cd15710
    Location:17 → 131
    ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
    cd15711
    Location:212 → 329
    ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    134373312..134428790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    132698463..132753940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IWS0.1 GenPept UniProtKB/Swiss-Prot:Q8IWS0

Gene LinkOut

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

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