U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 26147, updated on 2-Nov-2024

Summary

Go to the top of the page Help
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, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 8.7), ovary (RPKM 6.6) and 24 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
PHD finger protein 19
Names
polycomb like 3
polycomb-like protein 3
tudor domain containing 19B

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous