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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
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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
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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

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