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

    Gene ID: 23469, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (63635802..63726011)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (64781733..64872211)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. PHF3-specific antibody responses in over 60% of patients with glioblastoma multiforme. Struss AK, et al. Oncogene, 2001 Jul 12. PMID 11464277
    2. PHF3 expression is frequently reduced in glioma. Fischer U, et al. Cytogenet Cell Genet, 2001. PMID 11856869
    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. 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
    5. 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

    See all (82) 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)

    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
    		  
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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_2024_08

    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

    Gene LinkOut

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

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