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

Gene ID: 84295, updated on 17-Jun-2019

Summary

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
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

Genomic context

See PHF6 in Genome Data Viewer
Location:
Xq26.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (134373312..134428790)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (133507324..133562822)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 160 Neighboring gene 5'-nucleotidase domain containing 1 pseudogene Neighboring gene origin of replication in promoter/intron 1 of HPRT1 Neighboring gene hypoxanthine phosphoribosyltransferase 1 Neighboring gene ribosomal protein L36a pseudogene 54

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation PagePubMed

Pathways from BioSystems

  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC14797

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphoprotein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ribonucleoprotein complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
scaffold protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
tubulin binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
blastocyst hatching IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
condensed chromosome kinetochore IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
PHD finger protein 6
Names
PHD-like zinc finger protein
centromere protein 31

NCBI Reference Sequences (RefSeq)

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_001015877.2NP_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
    Q8IWS0
    Related
    ENSP00000359839.3, ENST00000370803.7
    Conserved Domains (2) summary
    cd15710
    Location:17131
    ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
    cd15711
    Location:212329
    ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)
  2. NM_032335.3NP_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/Swiss-Prot
    Q8IWS0
    Related
    ENSP00000359836.4, ENST00000370800.4
    Conserved Domains (2) summary
    cd15710
    Location:17131
    ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
    cl22851
    Location:213283
    PHD_SF; PHD finger superfamily
  3. NM_032458.3NP_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
    Q8IWS0
    Related
    ENSP00000329097.3, ENST00000332070.7
    Conserved Domains (2) summary
    cd15710
    Location:17131
    ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
    cd15711
    Location:212329
    ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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