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    PHF21B PHD finger protein 21B [ Homo sapiens (human) ]

    Gene ID: 112885, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PHF21Bprovided by HGNC
    Official Full Name
    PHD finger protein 21Bprovided by HGNC
    Primary source
    HGNC:HGNC:25161
    See related
    Ensembl:ENSG00000056487 MIM:616727; AllianceGenome:HGNC:25161
    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
    PHF4; BHC80L
    Summary
    Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis (RPKM 1.4), brain (RPKM 1.4) and 8 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF21B in Genome Data Viewer
    Location:
    22q13.31
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (44881162..45010005, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45364687..45493893, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (45277042..45405886, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene PRR5-ARHGAP8 readthrough Neighboring gene Rho GTPase activating protein 8 Neighboring gene uncharacterized LOC105373062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45255234-45255928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45259453-45260206 Neighboring gene uncharacterized LOC124905133 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:45264084-45265283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45265953-45266864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45283652-45284216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45286475-45286976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45290290-45291254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45291255-45292218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45328117-45328618 Neighboring gene ribosomal protein L6 pseudogene 28 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45334716-45335643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45338425-45339352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45340279-45341206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45348327-45349097 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45349098-45349867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45352179-45352948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45355867-45356450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45359222-45359844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45359845-45360468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45360469-45361090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45361091-45361714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45361715-45362336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45362337-45362959 Neighboring gene Sharpr-MPRA regulatory region 3533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45375229-45375808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45377983-45378603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45387215-45388036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45390633-45391132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45395779-45396638 Neighboring gene uncharacterized LOC101927551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45398138-45398996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45398997-45399855 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:45404265-45404866 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:45427253-45427890 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:45427891-45428528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45445441-45446014 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45447813-45448616 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45448617-45449421 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45449422-45450225 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:45468530-45469729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45489639-45490138 Neighboring gene Sharpr-MPRA regulatory region 5228 Neighboring gene Sharpr-MPRA regulatory region 5104 Neighboring gene NUP50 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:45559735-45560257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13874 Neighboring gene uncharacterized LOC105373064 Neighboring gene nucleoporin 50

    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. PHF21B overexpression promotes cancer stem cell-like traits in prostate cancer cells by activating the Wnt/β-catenin signaling pathway. Li Q, et al. J Exp Clin Cancer Res, 2017 Jun 23. PMID 28645312, Free PMC Article
    2. The PHF21B gene is associated with major depression and modulates the stress response. Wong ML, et al. Mol Psychiatry, 2017 Jul. PMID 27777418, Free PMC Article
    3. PHF21B as a candidate tumor suppressor gene in head and neck squamous cell carcinomas. Bertonha FB, et al. Mol Oncol, 2015 Feb. PMID 25454821, Free PMC Article
    4. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Mihalič F, et al. Nat Commun, 2023 Sep 13. PMID 37704626, Free PMC Article
    5. A genome annotation-driven approach to cloning the human ORFeome. Collins JE, et al. Genome Biol, 2004. PMID 15461802, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHF21B constitutively activated wnt/beta-catenin signaling by transcriptionally downregulating SFRP1 and SFRP2, which promotes prostate cancer stem cell-like phenotype.
      Title: PHF21B overexpression promotes cancer stem cell-like traits in prostate cancer cells by activating the Wnt/β-catenin signaling pathway.
    2. PHF21b variants contribute significantly to differences in the levels of expression of this gene in several brain areas, including the hippocampus. Furthermore, using an animal model of stress, we found that Phf21b hippocampal gene expression is significantly decreased in animals resilient to chronic restraint stress when compared with non-chronically stressed animals.
      Title: The PHF21B gene is associated with major depression and modulates the stress response.
    3. These data suggest that PHF21B is a novel tumor suppressor gene that can be inactivated by genetic and epigenetic mechanisms in the human cancer.
      Title: PHF21B as a candidate tumor suppressor gene in head and neck squamous cell carcinomas.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34161

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PHD finger protein 21B
    Names
    PHD finger protein 4

    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_001135862.3 → NP_001129334.1  PHD finger protein 21B isoform 2

      See identical proteins and their annotated locations for NP_001129334.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an additional 5' non-coding exon, and uses an alternate, in-frame, acceptor splice site at one of the internal coding exons compared to transcript variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK092243, AL049760, BC012187, Z83838
      Consensus CDS
      CCDS46727.1
      UniProtKB/TrEMBL
      A0A0S2Z665
      Conserved Domains (2) summary
      PRK10263
      Location:83 → 267
      PRK10263; DNA translocase FtsK; Provisional
      cd15524
      Location:312 → 354
      PHD_PHF21B; PHD finger found in PHD finger protein 21B (PHF21B)

    2. NM_001242450.2 → NP_001229379.1  PHD finger protein 21B isoform 3

      See identical proteins and their annotated locations for NP_001229379.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at an alternate start codon and uses an alternate, in-frame, acceptor splice site at one of the internal coding exons, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK297317, BC012187, Z83838
      Consensus CDS
      CCDS56234.1
      UniProtKB/Swiss-Prot
      Q96EK2
      UniProtKB/TrEMBL
      B1AHC5
      Related
      ENSP00000401294.2, ENST00000420689.2
      Conserved Domains (2) summary
      cd15524
      Location:300 → 342
      PHD_PHF21B; PHD finger found in PHD finger protein 21B (PHF21B)
      pfam11825
      Location:96 → 155
      Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

    3. NM_001284296.2 → NP_001271225.1  PHD finger protein 21B isoform 4

      See identical proteins and their annotated locations for NP_001271225.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in its 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream in-frame start codon, and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (4) is significantly shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK091480, AK297317, BC012187, CN311600
      Consensus CDS
      CCDS63504.1
      UniProtKB/TrEMBL
      B1AHC6
      Related
      ENSP00000401091.2, ENST00000414269.2
      Conserved Domains (1) summary
      cd15524
      Location:150 → 192
      PHD_PHF21B; PHD finger found in PHD finger protein 21B (PHF21B)

    4. NM_001413063.1 → NP_001399992.1  PHD finger protein 21B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL049760, Z83838
      UniProtKB/TrEMBL
      A0A0S2Z665
      Related
      ENSP00000487086.1, ENST00000629843.3

    5. NM_138415.5 → NP_612424.1  PHD finger protein 21B isoform 1

      See identical proteins and their annotated locations for NP_612424.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL049760, BC012187, Z83838
      Consensus CDS
      CCDS14061.1
      UniProtKB/Swiss-Prot
      B0QYW3, B0QYW4, B3KRU4, B7Z4F8, Q5TFL2, Q6ICC0, Q96EK2
      UniProtKB/TrEMBL
      A0A0S2Z6R3
      Related
      ENSP00000324403.5, ENST00000313237.10
      Conserved Domains (2) summary
      cd15524
      Location:354 → 396
      PHD_PHF21B; PHD finger found in PHD finger protein 21B (PHF21B)
      pfam11825
      Location:108 → 193
      Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

    RNA

    1. NR_134535.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in an internal exon and lacks an alternate internal exon compared to variant 1. 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)
      AK092243, BC012187, KU178844, Z83838
      Related
      ENST00000403565.6

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      44881162..45010005 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441109.1 → XP_047297065.1  PHD finger protein 21B isoform X1

      UniProtKB/TrEMBL
      B1AHC6

    2. XM_047441110.1 → XP_047297066.1  PHD finger protein 21B isoform X1

      UniProtKB/TrEMBL
      B1AHC6

    3. XM_011529855.2 → XP_011528157.1  PHD finger protein 21B isoform X2

      UniProtKB/TrEMBL
      A0A0S2Z615
      Conserved Domains (1) summary
      PRK10263
      Location:83 → 306
      PRK10263; DNA translocase FtsK; Provisional

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      45364687..45493893 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325053.1 → XP_054181028.1  PHD finger protein 21B isoform X1

      UniProtKB/TrEMBL
      B1AHC6

    2. XM_054325055.1 → XP_054181030.1  PHD finger protein 21B isoform X1

      UniProtKB/TrEMBL
      B1AHC6

    3. XM_054325054.1 → XP_054181029.1  PHD finger protein 21B isoform X2

      UniProtKB/TrEMBL
      A0A0S2Z615
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96EK2.1 GenPept UniProtKB/Swiss-Prot:Q96EK2

    Gene LinkOut

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

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