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    KPTN kaptin, actin binding protein [ Homo sapiens (human) ]

    Gene ID: 11133, updated on 5-Mar-2024

    Summary

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    Official Symbol
    KPTNprovided by HGNC
    Official Full Name
    kaptin, actin binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:6404
    See related
    Ensembl:ENSG00000118162 MIM:615620; AllianceGenome:HGNC:6404
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    2E4; KICS4; MRT41
    Summary
    This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in bone marrow (RPKM 1.7), testis (RPKM 1.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KPTN in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47475150..47485839, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50306001..50316700, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (47978407..47987476, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47905847-47906546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47906547-47907244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47920878-47921870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47921871-47922864 Neighboring gene Meis homeobox 3 Neighboring gene hESC enhancers GRCh37_chr19:47931091-47931659 and GRCh37_chr19:47931660-47932227 Neighboring gene Sharpr-MPRA regulatory region 169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47939851-47940352 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:47945299-47945446 Neighboring gene solute carrier family 8 member A2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47949904-47950829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47971701-47972200 Neighboring gene Sharpr-MPRA regulatory region 3844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14866 Neighboring gene NAPA antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48003933-48004487 Neighboring gene NSF attachment protein alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14867 Neighboring gene Sharpr-MPRA regulatory region 13246 Neighboring gene zinc finger protein 541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14868 Neighboring gene RNA, 7SL, cytoplasmic 322, pseudogene

    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. Pathogenic variants in KPTN, a rare cause of macrocephaly and intellectual disability. Pacio Miguez M, et al. Am J Med Genet A, 2020 Oct. PMID 32808430
    2. Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing. Thiffault I, et al. Cold Spring Harb Mol Case Stud, 2020 Jun. PMID 32358097, Free PMC Article
    3. An actin-associated protein present in the microtubule organizing center and the growth cones of PC-12 cells. Bearer EL. J Neurosci, 1992 Mar. PMID 1372044, Free PMC Article
    4. Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures. Baple EL, et al. Am J Hum Genet, 2014 Jan 2. PMID 24239382, Free PMC Article
    5. 2E4/Kaptin (KPTN)--a candidate gene for the hearing loss locus, DFNA4. Bearer EL, et al. Ann Hum Genet, 2000 May. PMID 11409409, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Nonsense variant in a consanguineous family expands the phenotype of KPTN gene-related syndrome to include hearing impairment.
      Title: Nonsense variant in a consanguineous family expands the phenotype of KPTN gene-related syndrome to include hearing impairment.
    2. Pathogenic variants in KPTN, a rare cause of macrocephaly and intellectual disability.
      Title: Pathogenic variants in KPTN, a rare cause of macrocephaly and intellectual disability.
    3. Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing.
      Title: Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing.
    4. identification of a protein complex (KICSTOR) that is composed of four proteins, KPTN, ITFG2, C12orf66 and SZT2, and that is required for amino acid or glucose deprivation to inhibit mTORC1 in cultured human cells
      Title: KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1.
    5. We have demonstrated that mutations in KPTN, encoding kaptin, cause a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures.
      Title: Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures.
    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
    Macrocephaly-developmental delay syndrome
    MedGen: C3810225 OMIM: 615637 GeneReviews: Not available
    		Compare labs

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to amino acid starvation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to amino acid starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to glucose starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of TORC1 signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of TORC1 signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to lysosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of KICSTOR complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of KICSTOR complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of KICSTOR complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of filamentous actin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in lamellipodium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lamellipodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in postsynaptic actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in stereocilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    KICSTOR complex protein kaptin
    Names
    actin-associated protein 2E4
    epididymis secretory sperm binding protein

    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.

    Genomic

    1. NG_034097.1 RefSeqGene

      Range
      5046..14115
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291296.2 → NP_001278225.1  KICSTOR complex protein kaptin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two consecutive exons in the 5' coding region, but maintains the reading frame, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AK298672, BG388698, DA129265, DR759729
      UniProtKB/Swiss-Prot
      Q9Y664
      Conserved Domains (1) summary
      pfam13517
      Location:261 → 328
      VCBS; Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella

    2. NM_007059.4 → NP_008990.2  KICSTOR complex protein kaptin isoform 1

      See identical proteins and their annotated locations for NP_008990.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF105369, AK023996, AK225419, DA129265
      Consensus CDS
      CCDS42583.1
      UniProtKB/Swiss-Prot
      B3KN86, B4DQ76, Q96GT1, Q9Y664
      UniProtKB/TrEMBL
      A0A384NLB4
      Related
      ENSP00000337850.2, ENST00000338134.8
      Conserved Domains (1) summary
      pfam13517
      Location:317 → 384
      VCBS; Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella

    RNA

    1. NR_111923.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an additional segment and an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF105369, AK298672, BG388698, DA129265
      Related
      ENST00000594208.5

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      47475150..47485839 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017026228.2 → XP_016881717.1  KICSTOR complex protein kaptin isoform X2

    2. XM_017026227.2 → XP_016881716.1  KICSTOR complex protein kaptin isoform X1

    3. XM_024451333.2 → XP_024307101.1  KICSTOR complex protein kaptin isoform X3

      Conserved Domains (1) summary
      pfam13517
      Location:317 → 384
      VCBS; Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      50306001..50316700 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319675.1 → XP_054175650.1  KICSTOR complex protein kaptin isoform X2

    2. XM_054319674.1 → XP_054175649.1  KICSTOR complex protein kaptin isoform X1

    3. XM_054319676.1 → XP_054175651.1  KICSTOR complex protein kaptin isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y664.2 GenPept UniProtKB/Swiss-Prot:Q9Y664

    Gene LinkOut

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

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