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PPP1R21 protein phosphatase 1 regulatory subunit 21 [ Homo sapiens (human) ]

Gene ID: 129285, updated on 11-Apr-2024

Summary

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Official Symbol
PPP1R21provided by HGNC
Official Full Name
protein phosphatase 1 regulatory subunit 21provided by HGNC
Primary source
HGNC:HGNC:30595
See related
Ensembl:ENSG00000162869 MIM:618159; AllianceGenome:HGNC:30595
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
Fy-2; FERRY2; KLRAQ1; CCDC128; NEDHFBA
Summary
Located in early endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 15.5), kidney (RPKM 15.1) and 25 other tissues See more
Orthologs
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Genomic context

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See PPP1R21 in Genome Data Viewer
Location:
2p16.3
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (48440766..48515386)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (48446714..48521263)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (48667905..48742525)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15744 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48541778-48542606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11479 Neighboring gene forkhead box N2 Neighboring gene RNA, U4 small nuclear 49, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48617307-48617446 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48628408-48628554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48674501-48675002 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48734957-48735731 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48735732-48736506 Neighboring gene RNA, U6 small nuclear 282, pseudogene Neighboring gene STON1-GTF2A1L readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48757286-48757833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48787383-48787921 Neighboring gene stonin 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48812672-48813306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48841993-48842496 Neighboring gene general transcription factor IIA subunit 1 like Neighboring gene TPT1 pseudogene 11

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
  • 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. A Homozygous PPP1R21 Splice Variant Associated with Severe Developmental Delay, Absence of Speech, and Muscle Weakness Leads to Activated Proteasome Function. Hentschel A, et al. Mol Neurobiol, 2023 May. PMID 36692708, Free PMC Article
  2. PPP1R21 homozygous null variants associated with developmental delay, muscle weakness, distinctive facial features, and brain abnormalities. Suleiman J, et al. Clin Genet, 2018 Oct. PMID 29808498
  3. Biallelic loss of function variants in PPP1R21 cause a neurodevelopmental syndrome with impaired endocytic function. Rehman AU, et al. Hum Mutat, 2019 Mar. PMID 30520571, Free PMC Article
  4. ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes. Boxer LD, et al. Genes Dev, 2014 Sep 15. PMID 25228645, Free PMC Article
  5. Docking motif-guided mapping of the interactome of protein phosphatase-1. Hendrickx A, et al. Chem Biol, 2009 Apr 24. PMID 19389623

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Homozygous PPP1R21 Splice Variant Associated with Severe Developmental Delay, Absence of Speech, and Muscle Weakness Leads to Activated Proteasome Function.
    Title: A Homozygous PPP1R21 Splice Variant Associated with Severe Developmental Delay, Absence of Speech, and Muscle Weakness Leads to Activated Proteasome Function.
  2. a role of PPP1R21 within the endosomal sorting process or endosome maturation pathway, is reported.
    Title: Biallelic loss of function variants in PPP1R21 cause a neurodevelopmental syndrome with impaired endocytic function.
  3. Although PPP1R21 has not yet been linked to human disease, the consistency in the phenotype of individuals from unrelated families, the nature of the variants which result in truncated proteins, and the expected vital role for PPP1R21 in cellular function, all support that PPP1R21 is a novel disease-associated gene responsible for the phenotype observed in these individuals
    Title: PPP1R21 homozygous null variants associated with developmental delay, muscle weakness, distinctive facial features, and brain abnormalities.
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

Associated conditions

Description Tests
Neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities
MedGen: C5543591 OMIM: 619383 GeneReviews: Not available
not available

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ16566, MGC111781

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 

General protein information

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Preferred Names
protein phosphatase 1 regulatory subunit 21
Names
KLRAQ motif containing 1
KLRAQ motif-containing protein 1
coiled-coil domain containing 128
coiled-coil domain-containing protein 128

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_001135629.3 → NP_001129101.1  protein phosphatase 1 regulatory subunit 21 isoform 1

    See identical proteins and their annotated locations for NP_001129101.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
    Source sequence(s)
    AA449986, AC093635, AK172762, AY134855, BC117279
    Consensus CDS
    CCDS46278.1
    UniProtKB/Swiss-Prot
    B7ZKY5, B7ZKY7, E1B6W7, Q2TA78, Q6ZMI0, Q6ZMI6, Q8IW83, Q8J029, Q96ES8
    Related
    ENSP00000294952.8, ENST00000294952.13
    Conserved Domains (3) summary
    pfam10205
    Location:11 → 111
    KLRAQ; Predicted coiled-coil domain-containing protein
    pfam10212
    Location:255 → 771
    TTKRSYEDQ; Predicted coiled-coil domain-containing protein
    cl25732
    Location:5 → 274
    SMC_N; RecF/RecN/SMC N terminal domain

  2. NM_001193475.2 → NP_001180404.1  protein phosphatase 1 regulatory subunit 21 isoform 5

    See identical proteins and their annotated locations for NP_001180404.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two alternate in-frame exons in the coding region, compared to variant 1. The resulting protein (isoform 5) is shorter than isoform 1.
    Source sequence(s)
    AA449986, AC093635, AK172762, AY134855, BC143466
    Consensus CDS
    CCDS54358.1
    UniProtKB/Swiss-Prot
    Q6ZMI0
    Related
    ENSP00000415696.2, ENST00000449090.6
    Conserved Domains (2) summary
    pfam10205
    Location:11 → 111
    KLRAQ; Predicted coiled-coil domain-containing protein
    pfam10212
    Location:255 → 729
    TTKRSYEDQ; Predicted coiled-coil domain-containing protein

  3. NM_152994.5 → NP_694539.1  protein phosphatase 1 regulatory subunit 21 isoform 2

    See identical proteins and their annotated locations for NP_694539.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AA449986, AC093635, AK172762, AY134855
    Consensus CDS
    CCDS1839.1
    UniProtKB/Swiss-Prot
    Q6ZMI0
    Related
    ENSP00000281394.4, ENST00000281394.8
    Conserved Domains (2) summary
    pfam10205
    Location:11 → 111
    KLRAQ; Predicted coiled-coil domain-containing protein
    pfam10212
    Location:255 → 760
    TTKRSYEDQ; Predicted coiled-coil domain-containing protein

RNA

  1. NR_024188.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA449986, AC093635, AK122900, AK172762, AY134855, BC117279
    Related
    ENST00000416913.5

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    48440766..48515386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443254.1 → XP_047299210.1  protein phosphatase 1 regulatory subunit 21 isoform X1

RNA

  1. XR_007069367.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    48446714..48521263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340461.1 → XP_054196436.1  protein phosphatase 1 regulatory subunit 21 isoform X1

RNA

  1. XR_008486266.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001135630.1: Suppressed sequence

    Description
    NM_001135630.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZMI0.1 GenPept UniProtKB/Swiss-Prot:Q6ZMI0

Gene LinkOut

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