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

    Gene ID: 129285, updated on 2-Nov-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
    Enables RNA binding activity. Located in early endosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.5), kidney (RPKM 15.1) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (48440766..48515386)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (48446714..48521263)
    RS_2024_09 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 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. Expanding the phenotype of PPP1R21-related neurodevelopmental disorder. Almannai M, et al. Clin Genet, 2024 Jun. PMID 38356149,
    3. 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
    4. 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
    5. The Rab5 effector FERRY links early endosomes with mRNA localization. Schuhmacher JS, et al. Mol Cell, 2023 Jun 1. PMID 37267905

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expanding the phenotype of PPP1R21-related neurodevelopmental disorder.
      Title: Expanding the phenotype of PPP1R21-related neurodevelopmental disorder.
    2. 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.
    3. 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.
    4. 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 RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    ferry endosomal RAB5 effector complex subunit 2

    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_2024_08

    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

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

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