U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 112885, updated on 3-Apr-2024

Summary

Go to the top of the page Help
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, Apr 2022]
Expression
Biased expression in testis (RPKM 1.4), brain (RPKM 1.4) and 8 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
Location:
22q13.31
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (44881162..45010005, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45364687..45493893, complement)
105.20220307 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

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
  • 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. 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. A genome annotation-driven approach to cloning the human ORFeome. Collins JE, et al. Genome Biol, 2004. PMID 15461802, Free PMC Article
  5. The DNA sequence of human chromosome 22. Dunham I, et al. Nature, 1999 Dec 2. PMID 10591208

See all (14) 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

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

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

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

  • FLJ34161

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
PHD finger protein 21B
Names
PHD finger protein 4

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_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
    B1AHC5
    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_2023_10

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
    B1AHC5

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

    UniProtKB/TrEMBL
    B1AHC5

  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
    B1AHC5

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

    UniProtKB/TrEMBL
    B1AHC5

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

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous