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PHF21A PHD finger protein 21A [ Homo sapiens (human) ]

Gene ID: 51317, updated on 26-Oct-2022

Summary

Official Symbol
PHF21Aprovided by HGNC
Official Full Name
PHD finger protein 21Aprovided by HGNC
Primary source
HGNC:HGNC:24156
See related
Ensembl:ENSG00000135365 MIM:608325; AllianceGenome:HGNC:24156
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
BHC80; NEDMS; BM-006; IDDBCS
Summary
The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]
Expression
Ubiquitous expression in testis (RPKM 7.2), ovary (RPKM 5.9) and 25 other tissues See more
Orthologs
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Genomic context

See PHF21A in Genome Data Viewer
Location:
11p11.2
Exon count:
25
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45929319..46121454, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46085233..46277451, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45950870..46143005, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene peroxisomal biogenesis factor 16 Neighboring gene LARGE xylosyl- and glucuronyltransferase 2 Neighboring gene Sharpr-MPRA regulatory region 8215 Neighboring gene uncharacterized LOC105376661 Neighboring gene FBLIM1 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-05-27)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated 2020-05-27)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1696

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of DNA repair complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
PHD finger protein 21A
Names
BHC80a
BRAF35-HDAC complex protein BHC80
BRAF35/HDAC2 complex (80 kDa)

NCBI Reference Sequences (RefSeq)

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_001101802.3NP_001095272.1  PHD finger protein 21A isoform a

    See identical proteins and their annotated locations for NP_001095272.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AC024475, AC068385
    Consensus CDS
    CCDS44578.1
    UniProtKB/Swiss-Prot
    Q96BD5, Q9NZE9
    Related
    ENSP00000398824.2, ENST00000418153.6
    Conserved Domains (2) summary
    COG5034
    Location:374536
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:490532
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  2. NM_001352025.3NP_001338954.1  PHD finger protein 21A isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c). Variants 3, 4, and 5 all encode isoform c.
    Source sequence(s)
    AC024475, AC068385
    Consensus CDS
    CCDS91465.1
    Conserved Domains (2) summary
    COG5034
    Location:375537
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:491533
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  3. NM_001352026.3NP_001338955.1  PHD finger protein 21A isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4), as well as variants 3 and 5, encodes isoform c.
    Source sequence(s)
    AC024475, AC068385
    Consensus CDS
    CCDS91465.1
    Conserved Domains (2) summary
    COG5034
    Location:375537
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:491533
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  4. NM_001352027.3NP_001338956.1  PHD finger protein 21A isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5), as well as variants 3 and 4, encodes isoform c.
    Source sequence(s)
    AC024475, AC068385
    Consensus CDS
    CCDS91465.1
    Related
    ENSP00000502222.1, ENST00000676320.1
    Conserved Domains (2) summary
    COG5034
    Location:375537
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:491533
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  5. NM_001352028.1NP_001338957.1  PHD finger protein 21A isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6), as well as variants 2 and 7, encodes isoform b.
    Source sequence(s)
    AC024475, AC068385
    Consensus CDS
    CCDS31474.1
    Conserved Domains (1) summary
    cd15523
    Location:444486
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  6. NM_001352029.1NP_001338958.1  PHD finger protein 21A isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7), as well as variants 2 and 6, encodes isoform b.
    Source sequence(s)
    AC024475, AC068385
    Consensus CDS
    CCDS31474.1
    Related
    ENSP00000508589.1, ENST00000690620.1
    Conserved Domains (1) summary
    cd15523
    Location:444486
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  7. NM_001352030.3NP_001338959.1  PHD finger protein 21A isoform 8

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8), as well as variants 9 and 10, encodes isoform d.
    Source sequence(s)
    AC024475, AC068385
    Conserved Domains (1) summary
    cd15523
    Location:443485
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  8. NM_001352031.3NP_001338960.1  PHD finger protein 21A isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9), as well as variants 8 and 10, encodes isoform d.
    Source sequence(s)
    AC024475, AC068385
    Conserved Domains (1) summary
    cd15523
    Location:443485
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  9. NM_001352032.3NP_001338961.1  PHD finger protein 21A isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10), as well as variants 8 and 9, encodes isoform d.
    Source sequence(s)
    AC024475, AC068385
    Conserved Domains (1) summary
    cd15523
    Location:443485
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  10. NM_016621.5NP_057705.3  PHD finger protein 21A isoform b

    See identical proteins and their annotated locations for NP_057705.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the mid-coding region, and includes an alternate in-frame exon in the 3' coding region, but lacks a different alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform b) is shorter than isoform a. Variants 2, 6, and 7 all encode the same isoform (b).
    Source sequence(s)
    AB051483, AC024475, AC068385
    Consensus CDS
    CCDS31474.1
    UniProtKB/Swiss-Prot
    Q96BD5
    Related
    ENSP00000323152.6, ENST00000323180.10
    Conserved Domains (1) summary
    cd15523
    Location:444486
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)

RNA

  1. NR_147890.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC024475, AC068385
  2. NR_165446.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC024475, AC068385

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    45929319..46121454 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427091.1XP_047283047.1  PHD finger protein 21A isoform X8

  2. XM_047427108.1XP_047283064.1  PHD finger protein 21A isoform X19

  3. XM_047427085.1XP_047283041.1  PHD finger protein 21A isoform X6

  4. XM_047427109.1XP_047283065.1  PHD finger protein 21A isoform X18

  5. XM_047427105.1XP_047283061.1  PHD finger protein 21A isoform X17

  6. XM_047427094.1XP_047283050.1  PHD finger protein 21A isoform X9

  7. XM_047427081.1XP_047283037.1  PHD finger protein 21A isoform X2

  8. XM_047427082.1XP_047283038.1  PHD finger protein 21A isoform X3

  9. XM_047427098.1XP_047283054.1  PHD finger protein 21A isoform X12

  10. XM_011520157.3XP_011518459.1  PHD finger protein 21A isoform X1

    See identical proteins and their annotated locations for XP_011518459.1

    Conserved Domains (2) summary
    cd15523
    Location:498540
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    cl26267
    Location:382544
    ING; Inhibitor of growth proteins N-terminal histone-binding
  11. XM_017017907.2XP_016873396.1  PHD finger protein 21A isoform X22

    Conserved Domains (3) summary
    COG5034
    Location:291453
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:407449
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    pfam01017
    Location:362
    STAT_alpha; STAT protein, all-alpha domain
  12. XM_047427090.1XP_047283046.1  PHD finger protein 21A isoform X8

  13. XM_017017892.2XP_016873381.1  PHD finger protein 21A isoform X6

    Conserved Domains (2) summary
    COG5034
    Location:374536
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:490532
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  14. XM_047427107.1XP_047283063.1  PHD finger protein 21A isoform X18

  15. XM_017017891.2XP_016873380.1  PHD finger protein 21A isoform X7

    UniProtKB/Swiss-Prot
    Q96BD5, Q9NZE9
    Conserved Domains (2) summary
    COG5034
    Location:374536
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:490532
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  16. XM_047427104.1XP_047283060.1  PHD finger protein 21A isoform X17

  17. XM_047427092.1XP_047283048.1  PHD finger protein 21A isoform X9

  18. XM_011520179.4XP_011518481.1  PHD finger protein 21A isoform X14

    See identical proteins and their annotated locations for XP_011518481.1

    UniProtKB/Swiss-Prot
    Q96BD5
    Conserved Domains (1) summary
    cd15523
    Location:444486
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  19. XM_017017889.2XP_016873378.1  PHD finger protein 21A isoform X2

    Conserved Domains (2) summary
    cd15523
    Location:497539
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    cl26267
    Location:381543
    ING; Inhibitor of growth proteins N-terminal histone-binding
  20. XM_011520158.3XP_011518460.1  PHD finger protein 21A isoform X1

    See identical proteins and their annotated locations for XP_011518460.1

    Conserved Domains (2) summary
    cd15523
    Location:498540
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    cl26267
    Location:382544
    ING; Inhibitor of growth proteins N-terminal histone-binding
  21. XM_047427087.1XP_047283043.1  PHD finger protein 21A isoform X6

  22. XM_047427102.1XP_047283058.1  PHD finger protein 21A isoform X15

    Related
    ENSP00000431964.2, ENST00000525676.6
  23. XM_047427110.1XP_047283066.1  PHD finger protein 21A isoform X18

  24. XM_047427089.1XP_047283045.1  PHD finger protein 21A isoform X7

    UniProtKB/Swiss-Prot
    Q9NZE9
  25. XM_005252965.5XP_005253022.1  PHD finger protein 21A isoform X5

    See identical proteins and their annotated locations for XP_005253022.1

    UniProtKB/Swiss-Prot
    Q96BD5
    Conserved Domains (2) summary
    COG5034
    Location:375537
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:491533
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  26. XM_047427101.1XP_047283057.1  PHD finger protein 21A isoform X14

  27. XM_017017887.3XP_016873376.1  PHD finger protein 21A isoform X1

    Conserved Domains (2) summary
    cd15523
    Location:498540
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    cl26267
    Location:382544
    ING; Inhibitor of growth proteins N-terminal histone-binding
  28. XM_011520175.3XP_011518477.1  PHD finger protein 21A isoform X6

    See identical proteins and their annotated locations for XP_011518477.1

    Conserved Domains (2) summary
    COG5034
    Location:374536
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:490532
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  29. XM_011520174.3XP_011518476.1  PHD finger protein 21A isoform X5

    See identical proteins and their annotated locations for XP_011518476.1

    UniProtKB/Swiss-Prot
    Q96BD5
    Conserved Domains (2) summary
    COG5034
    Location:375537
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15523
    Location:491533
    PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
  30. XM_047427093.1XP_047283049.1  PHD finger protein 21A isoform X9

  31. XM_047427100.1XP_047283056.1  PHD finger protein 21A isoform X14

  32. XM_047427088.1XP_047283044.1  PHD finger protein 21A isoform X6

  33. XM_047427084.1XP_047283040.1  PHD finger protein 21A isoform X5

  34. XM_047427079.1XP_047283035.1  PHD finger protein 21A isoform X1

  35. XM_047427086.1XP_047283042.1  PHD finger protein 21A isoform X7

    UniProtKB/Swiss-Prot
    Q9NZE9
  36. XM_047427080.1XP_047283036.1  PHD finger protein 21A isoform X1

  37. XM_047427103.1XP_047283059.1  PHD finger protein 21A isoform X16

  38. XM_047427083.1XP_047283039.1  PHD finger protein 21A isoform X4

  39. XM_047427097.1XP_047283053.1  PHD finger protein 21A isoform X11

  40. XM_047427099.1XP_047283055.1  PHD finger protein 21A isoform X13

  41. XM_047427095.1XP_047283051.1  PHD finger protein 21A isoform X10

  42. XM_047427113.1XP_047283069.1  PHD finger protein 21A isoform X21

  43. XM_047427111.1XP_047283067.1  PHD finger protein 21A isoform X20

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    46085233..46277451 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)