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    PHF19 PHD finger protein 19 [ Homo sapiens (human) ]

    Gene ID: 26147, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PHF19provided by HGNC
    Official Full Name
    PHD finger protein 19provided by HGNC
    Primary source
    HGNC:HGNC:24566
    See related
    Ensembl:ENSG00000119403 MIM:609740; AllianceGenome:HGNC:24566
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PCL3; MTF2L1; TDRD19B
    Summary
    Enables methylated histone binding activity. Involved in negative regulation of gene expression, epigenetic. Located in ESC/E(Z) complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 8.7), ovary (RPKM 6.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF19 in Genome Data Viewer
    Location:
    9q33.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (120855651..120904128, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (133051794..133091037, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (123617929..123657174, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr9:123587005-123587204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123595637-123596180 Neighboring gene proteasome 26S subunit, non-ATPase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123603211-123603712 Neighboring gene Sharpr-MPRA regulatory regions 2033 and 13781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123618013-123618514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123618515-123619014 Neighboring gene cutA divalent cation tolerance like, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20224 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:123635243-123635866 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:123635867-123636492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:123638303-123638894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28901 Neighboring gene CRISPRi-validated cis-regulatory element chr9.2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123675790-123676294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123687703-123688226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28909 Neighboring gene TNF receptor associated factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28912 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:123725569-123725752 Neighboring gene C5 3' UTR overlapping transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28913 Neighboring gene complement C5 Neighboring gene uncharacterized LOC124902261

    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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    Related articles in PubMed

    1. hPCL3s Promotes Hepatocellular Carcinoma Metastasis by Activating β-Catenin Signaling. Cai Z, et al. Cancer Res, 2018 May 15. PMID 29483096
    2. Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Mason MJ, et al. Leukemia, 2020 Jul. PMID 32060406, Free PMC Article
    3. PHD finger protein 19 expression in multiple myeloma: Association with clinical features, induction therapy outcome, disease progression, and survival. Li Y, et al. J Clin Lab Anal, 2021 Sep. PMID 34390275, Free PMC Article
    4. 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma. Johnson TS, et al. Nat Commun, 2024 May 16. PMID 38755140, Free PMC Article
    5. Downregulation of PHF19 inhibits cell growth and migration in gastric cancer. Wang H, et al. Scand J Gastroenterol, 2020 Jun. PMID 32449434

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma.
      Title: 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma.
    2. Regulation of hPCL3 isoforms' ubiquitination by TRIM21 in non-small cell lung cancer progression.
      Title: Regulation of hPCL3 isoforms' ubiquitination by TRIM21 in non-small cell lung cancer progression.
    3. PHD finger protein 19 expression in multiple myeloma: Association with clinical features, induction therapy outcome, disease progression, and survival.
      Title: PHD finger protein 19 expression in multiple myeloma: Association with clinical features, induction therapy outcome, disease progression, and survival.
    4. PHF19 inhibition as a therapeutic target in multiple myeloma.
      Title: PHF19 inhibition as a therapeutic target in multiple myeloma.
    5. PHF19 activates hedgehog signaling and promotes tumorigenesis in hepatocellular carcinoma.
      Title: PHF19 activates hedgehog signaling and promotes tumorigenesis in hepatocellular carcinoma.
    6. LINC_00355 promotes gastric cancer progression by upregulating PHF19 expression through sponging miR-15a-5p.
      Title: LINC_00355 promotes gastric cancer progression by upregulating PHF19 expression through sponging miR-15a-5p.
    7. Downregulation of PHF19 inhibits cell growth and migration in gastric cancer.
      Title: Downregulation of PHF19 inhibits cell growth and migration in gastric cancer.
    8. Polycomb-like Protein 3 Induces Proliferation and Drug Resistance in Multiple Myeloma and Is Regulated by miRNA-15a.
      Title: Polycomb-like Protein 3 Induces Proliferation and Drug Resistance in Multiple Myeloma and Is Regulated by miRNA-15a.
    9. PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells.
      Title: PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells.
    10. Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease.
      Title: Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
    EBI GWAS Catalog
    Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
    EBI GWAS Catalog
    REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis.
    EBI GWAS Catalog

    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

    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

    • MGC23929, MGC131698, MGC149712, MGC149713

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of gene expression, epigenetic IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of ESC/E(Z) complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    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 19
    Names
    polycomb like 3
    polycomb-like protein 3
    tudor domain containing 19B

    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)

    1. NM_001009936.3 → NP_001009936.1  PHD finger protein 19 isoform b

      See identical proteins and their annotated locations for NP_001009936.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate exon structure in both the 5' and 3' regions, and it thus differs in both UTRs, initiates translation from a downstream in-frame start codon, and includes an alternate 3' coding region, compared to variant 3. The encoded isoform (b, also known as hPCL3S) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform c.
      Source sequence(s)
      AI369987, BC022374
      Consensus CDS
      CCDS35117.1
      UniProtKB/Swiss-Prot
      Q5T6S3
      Related
      ENSP00000310372.6, ENST00000312189.10
      Conserved Domains (2) summary
      smart00333
      Location:38 → 87
      TUDOR; Tudor domain
      cd15579
      Location:98 → 150
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)

    2. NM_001286840.1 → NP_001273769.1  PHD finger protein 19 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
      Source sequence(s)
      AI193743, AK303433, BC044224, BU632411, BX640713
      Consensus CDS
      CCDS75889.1
      UniProtKB/TrEMBL
      A0A087X169, B3KV88
      Related
      ENSP00000483946.1, ENST00000616568.5
      Conserved Domains (4) summary
      smart00333
      Location:57 → 106
      TUDOR; Tudor domain
      cd15579
      Location:117 → 169
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
      cd15581
      Location:216 → 267
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
      pfam14061
      Location:550 → 596
      Mtf2_C; Polycomb-like MTF2 factor 2

    3. NM_001286842.1 → NP_001273771.1  PHD finger protein 19 isoform d

      See identical proteins and their annotated locations for NP_001273771.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks several 5' exons but includes an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 3. The encoded isoform (d) is shorter at the N-terminus, compared to isoform c.
      Source sequence(s)
      AI193743, AK302996, BC044224, BU632411, HY013521
      Consensus CDS
      CCDS69648.1
      UniProtKB/TrEMBL
      B7Z887, F5H8K3
      Related
      ENSP00000407433.1, ENST00000419155.5
      Conserved Domains (2) summary
      pfam14061
      Location:322 → 369
      Mtf2_C; Polycomb-like MTF2 factor 2
      cl22851
      Location:1 → 39
      PHD_SF; PHD finger superfamily

    4. NM_001286843.2 → NP_001273772.1  PHD finger protein 19 isoform e

      See identical proteins and their annotated locations for NP_001273772.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains alternate exon structure in both the 5' and 3' regions, and it thus differs in both UTRs, initiates translation from a downstream in-frame start codon, and includes an alternate 3' coding region, compared to variant 3. The encoded isoform (e) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform c.
      Source sequence(s)
      AI369987, BC022374, BC108663
      UniProtKB/TrEMBL
      X6RER8
      Related
      ENSP00000397935.1, ENST00000456291.1
      Conserved Domains (2) summary
      smart00333
      Location:38 → 87
      TUDOR; Tudor domain
      cl22851
      Location:98 → 124
      PHD_SF; PHD finger superfamily

    5. NM_015651.3 → NP_056466.1  PHD finger protein 19 isoform a

      See identical proteins and their annotated locations for NP_056466.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) uses an alternate 5' terminal exon and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 3. The encoded isoform (a, also known as hPCL3L) is shorter at the N-terminus, compared to isoform c.
      Source sequence(s)
      AI193743, BC044224, BC125076, BM784783, BU632411
      Consensus CDS
      CCDS35116.1
      UniProtKB/Swiss-Prot
      Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
      UniProtKB/TrEMBL
      B3KV88
      Related
      ENSP00000363003.3, ENST00000373896.8
      Conserved Domains (4) summary
      cd15579
      Location:98 → 150
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
      cd15581
      Location:197 → 248
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
      pfam14061
      Location:531 → 578
      Mtf2_C; Polycomb-like MTF2 factor 2
      cd20451
      Location:39 → 95
      Tudor_PHF19; Tudor domain found in PHD finger protein1 (PHF19) and similar proteins

    RNA

    1. NR_104601.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks several 5' exons but includes an alternate 5' terminal exon, and it also lacks an alternate exon in the 3' region, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI193743, BC044224, BU632411, HY013521

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      120855651..120904128 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014612.3 → XP_016870101.1  PHD finger protein 19 isoform X2

      UniProtKB/Swiss-Prot
      Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
      UniProtKB/TrEMBL
      B3KV88
      Conserved Domains (4) summary
      cd15579
      Location:98 → 150
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
      cd15581
      Location:197 → 248
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
      pfam14061
      Location:531 → 578
      Mtf2_C; Polycomb-like MTF2 factor 2
      cd20451
      Location:39 → 95
      Tudor_PHF19; Tudor domain found in PHD finger protein1 (PHF19) and similar proteins

    2. XM_005251906.4 → XP_005251963.2  PHD finger protein 19 isoform X1

    3. XM_011518509.4 → XP_011516811.1  PHD finger protein 19 isoform X2

      See identical proteins and their annotated locations for XP_011516811.1

      UniProtKB/Swiss-Prot
      Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
      UniProtKB/TrEMBL
      B3KV88
      Conserved Domains (4) summary
      cd15579
      Location:98 → 150
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
      cd15581
      Location:197 → 248
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
      pfam14061
      Location:531 → 578
      Mtf2_C; Polycomb-like MTF2 factor 2
      cd20451
      Location:39 → 95
      Tudor_PHF19; Tudor domain found in PHD finger protein1 (PHF19) and similar proteins

    4. XM_047423211.1 → XP_047279167.1  PHD finger protein 19 isoform X5

    5. XM_024447507.2 → XP_024303275.1  PHD finger protein 19 isoform X5

      UniProtKB/TrEMBL
      B7Z887
      Conserved Domains (2) summary
      cd15581
      Location:24 → 75
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
      pfam14061
      Location:358 → 405
      Mtf2_C; Polycomb-like MTF2 factor 2

    6. XM_047423210.1 → XP_047279166.1  PHD finger protein 19 isoform X3

    7. XM_011518515.3 → XP_011516817.1  PHD finger protein 19 isoform X4

      Conserved Domains (3) summary
      smart00333
      Location:57 → 106
      TUDOR; Tudor domain
      cd15579
      Location:117 → 169
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
      cd15581
      Location:216 → 267
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)

    8. XM_011518516.3 → XP_011516818.1  PHD finger protein 19 isoform X6

      Conserved Domains (3) summary
      smart00333
      Location:57 → 106
      TUDOR; Tudor domain
      cd15579
      Location:117 → 169
      PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
      cd15581
      Location:216 → 267
      PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      133051794..133091037 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362697.1 → XP_054218672.1  PHD finger protein 19 isoform X2

      UniProtKB/Swiss-Prot
      Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9

    2. XM_054362698.1 → XP_054218673.1  PHD finger protein 19 isoform X2

      UniProtKB/Swiss-Prot
      Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9

    3. XM_054362701.1 → XP_054218676.1  PHD finger protein 19 isoform X5

    4. XM_054362702.1 → XP_054218677.1  PHD finger protein 19 isoform X5

    5. XM_054362699.1 → XP_054218674.1  PHD finger protein 19 isoform X3

    6. XM_054362700.1 → XP_054218675.1  PHD finger protein 19 isoform X4

    7. XM_054362703.1 → XP_054218678.1  PHD finger protein 19 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T6S3.1 GenPept UniProtKB/Swiss-Prot:Q5T6S3

    Gene LinkOut

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

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