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PHF3 PHD finger protein 3 [ Homo sapiens (human) ]

Gene ID: 23469, updated on 5-Mar-2024

Summary

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Official Symbol
PHF3provided by HGNC
Official Full Name
PHD finger protein 3provided by HGNC
Primary source
HGNC:HGNC:8921
See related
Ensembl:ENSG00000118482 MIM:607789; AllianceGenome:HGNC:8921
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
Summary
This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Expression
Ubiquitous expression in testis (RPKM 15.6), thyroid (RPKM 14.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PHF3 in Genome Data Viewer
Location:
6q12
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (63635802..63726011)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (64781733..64872211)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (64345707..64435904)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene lengsin, lens protein with glutamine synthetase domain Neighboring gene translation initiation factor IF-2-like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282109-64282844 Neighboring gene uncharacterized LOC128125822 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282845-64283580 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64283581-64284316 Neighboring gene Sharpr-MPRA regulatory region 1413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24721 Neighboring gene NANOG hESC enhancer GRCh37_chr6:64344395-64344932 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64345464-64346284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24722 Neighboring gene protein tyrosine phosphatase 4A1 Neighboring gene ribosomal protein L9 pseudogene 18 Neighboring gene platelet activating factor acetylhydrolase 1b regulatory subunit 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24723 Neighboring gene eyes shut homolog Neighboring gene S-phase cancer associated transcript 8

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
  • 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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Related articles in PubMed

  1. PHF3 expression is frequently reduced in glioma. Fischer U, et al. Cytogenet Cell Genet, 2001. PMID 11856869
  2. PHF3-specific antibody responses in over 60% of patients with glioblastoma multiforme. Struss AK, et al. Oncogene, 2001 Jul 12. PMID 11464277
  3. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Appel LM, et al. Nat Commun, 2021 Oct 19. PMID 34667177, Free PMC Article
  4. A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study. Zuo L, et al. PLoS One, 2011. PMID 22096494, Free PMC Article
  5. Autoantibodies against GLEA2 and PHF3 in glioblastoma: tumor-associated autoantibodies correlated with prolonged survival. Pallasch CP, et al. Int J Cancer, 2005 Nov 10. PMID 15906353

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
    Title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
  2. We confirmed with our previous findings that PTP4A1-PHF3-EYS variants were significantly associated with alcohol dependence.
    Title: Common PTP4A1-PHF3-EYS variants are specific for alcohol dependence.
  3. PTP4A1-PHF3-EYS variants were associated with alcohol dependence.
    Title: Association of rare PTP4A1-PHF3-EYS variants with alcohol dependence.
  4. Data conclude that the PHF3-PTP4A1 region appears to harbor a causal locus for alcohol dependence, and proteins encoded by PHF3 and/or PTP4A1 might play a functional role in the disorder.
    Title: A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.
  5. Survival of patients with GLEA2 antibodies was increased to 17.4 months and for patients with PHF3 antibodies to 14.7 months, as compared to 7.2 months for patients without GLEA2 or PHF3 antibodies in glioblastoma.
    Title: Autoantibodies against GLEA2 and PHF3 in glioblastoma: tumor-associated autoantibodies correlated with prolonged survival.
  6. novel member of a large class of regulatory proteins containing a LAP motif, and loss of its expression in glioblastoma may contribute to glioma development
    Title: PHF3 expression is frequently reduced in glioma.
Submit: New GeneRIF Correction

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-02-27)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2019-02-27)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of PHD finger protein 3 (PHF3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl 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

Homology

Clone Names

  • KIAA0244, MGC142210, MGC142212

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
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 3

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_034034.2 RefSeqGene

    Range
    5002..95211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290259.2 → NP_001277188.1  PHD finger protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001277188.1

    Status: REVIEWED

    Source sequence(s)
    AL354719, AL513043
    UniProtKB/Swiss-Prot
    Q92576
    UniProtKB/TrEMBL
    B3KP41
    Conserved Domains (6) summary
    smart00510
    Location:841 → 941
    TFS2M; Domain in the central regions of transcription elongation factor S-II (and elsewhere)
    PHA03369
    Location:916 → 1117
    PHA03369; capsid maturational protease; Provisional
    TIGR01385
    Location:760 → 963
    TFSII; transcription elongation factor S-II
    cd15638
    Location:631 → 681
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam08648
    Location:1831 → 1945
    DUF1777; Protein of unknown function (DUF1777)
    pfam07744
    Location:1114 → 1260
    SPOC; SPOC domain

  2. NM_001290260.2 → NP_001277189.1  PHD finger protein 3 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL354719, AL513043
    Consensus CDS
    CCDS78155.1
    UniProtKB/TrEMBL
    A8K376, D6R9X2
    Related
    ENSP00000422841.1, ENST00000509330.5

  3. NM_001370348.2 → NP_001357277.1  PHD finger protein 3 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL354719, AL513043
    Consensus CDS
    CCDS4966.1
    UniProtKB/Swiss-Prot
    A3KFI8, Q14CR5, Q5CZI1, Q5T1T6, Q92576, Q9NQ16, Q9UI45
    Related
    ENSP00000262043.4, ENST00000262043.8
    Conserved Domains (7) summary
    smart00510
    Location:929 → 1029
    TFS2M; Domain in the central regions of transcription elongation factor S-II (and elsewhere)
    PHA03369
    Location:1004 → 1205
    PHA03369; capsid maturational protease; Provisional
    PTZ00112
    Location:1481 → 1708
    PTZ00112; origin recognition complex 1 protein; Provisional
    TIGR01385
    Location:848 → 1051
    TFSII; transcription elongation factor S-II
    cd15638
    Location:719 → 769
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam08648
    Location:1919 → 2033
    DUF1777; Protein of unknown function (DUF1777)
    pfam07744
    Location:1202 → 1348
    SPOC; SPOC domain

  4. NM_001370349.2 → NP_001357278.1  PHD finger protein 3 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL354719, AL513043
    Conserved Domains (6) summary
    smart00510
    Location:841 → 941
    TFS2M; Domain in the central regions of transcription elongation factor S-II (and elsewhere)
    PHA03369
    Location:916 → 1117
    PHA03369; capsid maturational protease; Provisional
    TIGR01385
    Location:760 → 963
    TFSII; transcription elongation factor S-II
    cd15638
    Location:631 → 681
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam08648
    Location:1831 → 1945
    DUF1777; Protein of unknown function (DUF1777)
    pfam07744
    Location:1114 → 1260
    SPOC; SPOC domain

  5. NM_001370350.2 → NP_001357279.1  PHD finger protein 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL354719, AL513043
    Conserved Domains (6) summary
    smart00510
    Location:198 → 298
    TFS2M; Domain in the central regions of transcription elongation factor S-II (and elsewhere)
    PHA03369
    Location:273 → 474
    PHA03369; capsid maturational protease; Provisional
    PTZ00112
    Location:750 → 977
    PTZ00112; origin recognition complex 1 protein; Provisional
    TIGR01622
    Location:1200 → 1308
    SF-CC1; splicing factor, CC1-like family
    pfam07744
    Location:471 → 617
    SPOC; SPOC domain
    cl22851
    Location:1 → 38
    PHD_SF; PHD finger superfamily

  6. NM_015153.4 → NP_055968.1  PHD finger protein 3 isoform 1

    See identical proteins and their annotated locations for NP_055968.1

    Status: REVIEWED

    Source sequence(s)
    AL354719
    Consensus CDS
    CCDS4966.1
    UniProtKB/Swiss-Prot
    A3KFI8, Q14CR5, Q5CZI1, Q5T1T6, Q92576, Q9NQ16, Q9UI45
    Related
    ENSP00000377048.1, ENST00000393387.5
    Conserved Domains (7) summary
    smart00510
    Location:929 → 1029
    TFS2M; Domain in the central regions of transcription elongation factor S-II (and elsewhere)
    PHA03369
    Location:1004 → 1205
    PHA03369; capsid maturational protease; Provisional
    PTZ00112
    Location:1481 → 1708
    PTZ00112; origin recognition complex 1 protein; Provisional
    TIGR01385
    Location:848 → 1051
    TFSII; transcription elongation factor S-II
    cd15638
    Location:719 → 769
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam08648
    Location:1919 → 2033
    DUF1777; Protein of unknown function (DUF1777)
    pfam07744
    Location:1202 → 1348
    SPOC; SPOC domain

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    63635802..63726011
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535648.4 → XP_011533950.1  PHD finger protein 3 isoform X1

    Conserved Domains (5) summary
    cd15638
    Location:728 → 778
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:934 → 1044
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:1218 → 1324
    SPOC; SPOC domain
    pfam08648
    Location:1954 → 2048
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:1941 → 2035
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term

  2. XM_047418529.1 → XP_047274485.1  PHD finger protein 3 isoform X2

  3. XM_047418528.1 → XP_047274484.1  PHD finger protein 3 isoform X2

  4. XM_047418530.1 → XP_047274486.1  PHD finger protein 3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    64781733..64872211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354941.1 → XP_054210916.1  PHD finger protein 3 isoform X1

  2. XM_054354942.1 → XP_054210917.1  PHD finger protein 3 isoform X2

  3. XM_054354944.1 → XP_054210919.1  PHD finger protein 3 isoform X2

  4. XM_054354943.1 → XP_054210918.1  PHD finger protein 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92576.3 GenPept UniProtKB/Swiss-Prot:Q92576

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