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KPTN Gene(Protein Coding)

Kaptin, Actin Binding Protein

GCID:
GC19M047475
GIFtS:
45
Genes Participants
UDN Logo

Aliases for KPTN Gene

Aliases for KPTN Gene

  • Kaptin, Actin Binding Protein 2 3 5
  • Actin-Associated Protein 2E4 3 4
  • Kaptin (Actin-Binding Protein) 2
  • KICSTOR Complex Protein Kaptin 3
  • Kaptin 3
  • MRT41 3
  • 2E4 3

External Ids for KPTN Gene

Previous GeneCards Identifiers for KPTN Gene

  • GC19M048625
  • GC19M048369
  • GC19M052654
  • GC19M052670
  • GC19M052657
  • GC19M047978
  • GC19M044406

Summaries for KPTN Gene

Entrez Gene Summary for KPTN Gene

  • 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]

GeneCards Summary for KPTN Gene

KPTN (Kaptin, Actin Binding Protein) is a Protein Coding gene. Diseases associated with KPTN include Mental Retardation, Autosomal Recessive 41 and Pervasive Developmental Disorder. Gene Ontology (GO) annotations related to this gene include actin binding.

UniProtKB/Swiss-Prot for KPTN Gene

  • As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the RAG GTPases. Functions upstream of the RAG GTPases and is required to negatively regulate mTORC1 signaling in absence of amino acids. In absence of the KICSTOR complex mTORC1 is constitutively localized to the lysosome and activated. The KICSTOR complex is also probably involved in the regulation of mTORC1 by glucose.

Gene Wiki entry for KPTN Gene

Additional gene information for KPTN Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KPTN Gene

Genomics for KPTN Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for KPTN Gene

Promoters and enhancers for KPTN Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH19I047483 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 556.3 +2.1 2145 2.5 HDGF SMAD1 ARNT SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 ZNF213 KPTN NAPA-AS1 ZC3H4 BICRA GRWD1 ENSG00000268746 NOP53 NOP53-AS1 EHD2 CYTH2
GH19I047486 Enhancer 1 Ensembl ENCODE dbSUPER 557.8 -0.8 -759 1.8 ZFHX2 POLR2A MAX EBF1 MNT MYC RUNX3 EGR2 KPTN ENSG00000279861 NAPA-AS1 NAPA
GH19I047487 Enhancer 0.5 ENCODE dbSUPER 550.8 +0.4 372 0.2 RUNX3 KPTN NAPA-AS1
GH19I047509 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 7.3 -26.2 -26152 7.1 HDGF FOXA2 PKNOX1 CLOCK MLX ARNT ARID4B SIN3A ZNF2 ZBTB7B NAPA ZC3H4 BICRA GRWD1 NOP53-AS1 KDELR1 KPTN CCDC9 C5AR1 DHX34
GH19I047607 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 5.8 -124.3 -124278 6.9 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B ZNF207 ZNF143 BICRA ZNF541 ZC3H4 MEIS3 PRKD2 CCDC9 LIG1 KPTN ENSG00000268746 ENSG00000277383
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KPTN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KPTN gene promoter:

Genomic Locations for KPTN Gene

Genomic Locations for KPTN Gene
chr19:47,475,141-47,486,791
(GRCh38/hg38)
Size:
11,651 bases
Orientation:
Minus strand
chr19:47,978,400-47,987,525
(GRCh37/hg19)

Genomic View for KPTN Gene

Genes around KPTN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KPTN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KPTN Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for KPTN Gene

Proteins for KPTN Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for KPTN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y664-KPTN_HUMAN
    Recommended name:
    KICSTOR complex protein kaptin
    Protein Accession:
    Q9Y664
    Secondary Accessions:
    • B3KN86
    • B4DQ76
    • Q96GT1

    Protein attributes for KPTN Gene

    Size:
    436 amino acids
    Molecular mass:
    48080 Da
    Quaternary structure:
    • Part of the KICSTOR complex composed of KPTN, ITFG2, C12orf66 and SZT2. SZT2 probably serves as a link between the other three proteins in the KICSTOR complex and mediates the direct interaction with the GATOR1 complex (PubMed:28199306). May associate with F-actin filaments (PubMed:10099934).
    SequenceCaution:
    • Sequence=AAD39358.1; Type=Frameshift; Positions=8, 14, 410, 419; Evidence={ECO:0000305};

    Alternative splice isoforms for KPTN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KPTN Gene

Protein Expression for KPTN Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for KPTN Gene

No Post-translational modifications

Other Protein References for KPTN Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KPTN Gene

Domains & Families for KPTN Gene

Gene Families for KPTN Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for KPTN Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for KPTN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with KPTN: view

No data available for UniProtKB/Swiss-Prot for KPTN Gene

Function for KPTN Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for KPTN Gene

UniProtKB/Swiss-Prot Function:
As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the RAG GTPases. Functions upstream of the RAG GTPases and is required to negatively regulate mTORC1 signaling in absence of amino acids. In absence of the KICSTOR complex mTORC1 is constitutively localized to the lysosome and activated. The KICSTOR complex is also probably involved in the regulation of mTORC1 by glucose.

Phenotypes From GWAS Catalog for KPTN Gene

Gene Ontology (GO) - Molecular Function for KPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051015 actin filament binding IDA 10099934
genes like me logo Genes that share ontologies with KPTN: view
genes like me logo Genes that share phenotypes with KPTN: view

Human Phenotype Ontology for KPTN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for KPTN Gene

MGI Knock Outs for KPTN:
  • Kptn tm1a(EUCOMM)Wtsi

Animal Model Products

CRISPR Products

miRNA for KPTN Gene

miRTarBase miRNAs that target KPTN

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for KPTN Gene

Localization for KPTN Gene

Subcellular locations from UniProtKB/Swiss-Prot for KPTN Gene

Lysosome membrane. Cell projection, lamellipodium. Cell projection, stereocilium. Note=Localization to lysosomes is amino acid-independent (PubMed:28199306). Colocalizes with F-actin (PubMed:24239382). {ECO:0000269 PubMed:24239382, ECO:0000269 PubMed:28199306}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KPTN gene
Compartment Confidence
cytoskeleton 5
nucleus 3
cytosol 3
lysosome 3
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA --
GO:0015629 actin cytoskeleton IEA --
GO:0016020 membrane IEA --
GO:0030027 lamellipodium IDA,IEA 10099934
genes like me logo Genes that share ontologies with KPTN: view

Pathways & Interactions for KPTN Gene

SuperPathways for KPTN Gene

PathCards logo More details on SuperPathways for KPTN
No Data Available

Gene Ontology (GO) - Biological Process for KPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization IEA --
GO:0034198 cellular response to amino acid starvation IMP 28199306
GO:0042149 cellular response to glucose starvation IMP 28199306
GO:0061462 protein localization to lysosome IMP 28199306
GO:1904262 negative regulation of TORC1 signaling IMP 28199306
genes like me logo Genes that share ontologies with KPTN: view

No data available for Pathways by source and SIGNOR curated interactions for KPTN Gene

Drugs & Compounds for KPTN Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for KPTN Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for KPTN Gene

(7) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(98) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for KPTN Gene

Kaptin (actin binding protein):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for KPTN Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14
SP1: - - -
SP2: - - - - -
SP3: - - - - -
SP4:
SP5: - -

Relevant External Links for KPTN Gene

GeneLoc Exon Structure for
KPTN
ECgene alternative splicing isoforms for
KPTN

Expression for KPTN Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KPTN Gene

mRNA expression in normal human tissues for KPTN Gene
mRNA expression by BioGPS for KPTN GenemRNA expression by GTEx for KPTN Gene

Protein differential expression in normal tissues from HIPED for KPTN Gene

This gene is overexpressed in Ovary (49.5) and Islet of Langerhans (15.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KPTN Gene



Protein tissue co-expression partners for KPTN Gene

NURSA nuclear receptor signaling pathways regulating expression of KPTN Gene:

KPTN

SOURCE GeneReport for Unigene cluster for KPTN Gene:

Hs.25441

Evidence on tissue expression from TISSUES for KPTN Gene

  • Muscle(4.2)
  • Nervous system(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for KPTN Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
  • tooth
Limb:
  • digit
  • finger
  • hand
  • upper limb
General:
  • skin
genes like me logo Genes that share expression patterns with KPTN: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for KPTN Gene

Orthologs for KPTN Gene

This gene was present in the common ancestor of chordates.

Orthologs for KPTN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia KPTN 34
  • 98 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia KPTN 33 34
  • 90.52 (n)
cow
(Bos Taurus)
 Mammalia KPTN 33 34
  • 89.14 (n)
mouse
(Mus musculus)
 Mammalia Kptn 33 16 34
  • 84.19 (n)
oppossum
(Monodelphis domestica)
 Mammalia KPTN 34
  • 76 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia KPTN 34
  • 73 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia KPTN 34
  • 63 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia kptn 33
  • 72.81 (n)
Str.12230 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.25661 33
zebrafish
(Danio rerio)
 Actinopterygii kptn 33 34
  • 62.6 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 30 (a)
 OneToOne
Species where no ortholog for KPTN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for KPTN Gene

ENSEMBL:
Gene Tree for KPTN (if available)
TreeFam:
Gene Tree for KPTN (if available)

Paralogs for KPTN Gene

No data available for Paralogs for KPTN Gene

Variants for KPTN Gene

Sequence variations from dbSNP and Humsavar for KPTN Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1046273 benign, Mental retardation, autosomal recessive 41 47,475,482(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs142867197 uncertain-significance, not specified, not provided, Mental retardation, autosomal recessive 41 47,483,973(-) C/G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs182019900 benign, likely-benign, not specified, not provided, Mental retardation, autosomal recessive 41 47,480,376(-) C/G/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs199648809 uncertain-significance, Mental retardation, autosomal recessive 41 47,476,834(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs374298314 pathogenic, Mental retardation, autosomal recessive 41, not provided 47,479,874(-) G/A/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for KPTN Gene

Variant ID Type Subtype PubMed ID
esv2758765 CNV loss 17122850
nsv1056887 CNV gain 25217958
nsv1143921 CNV deletion 24896259
nsv428366 CNV loss 18775914
nsv579888 CNV gain 21841781

Variation tolerance for KPTN Gene

Residual Variation Intolerance Score: 42.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.98; 36.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KPTN Gene

Human Gene Mutation Database (HGMD)
KPTN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KPTN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KPTN Gene

Disorders for KPTN Gene

MalaCards: The human disease database

(2) MalaCards diseases for KPTN Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal recessive 41
  • mrt41
pervasive developmental disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards
Search KPTN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

KPTN_HUMAN
  • Mental retardation, autosomal recessive 41 (MRT41) [MIM:615637]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT41 most consistent features are global developmental delay, macrocephaly with frontal bossing, high levels of anxiety, and some features suggestive of a pervasive developmental disorder. Less common features include fifth finger clinodactyly, recurrent pneumonia, and hepatosplenomegaly. {ECO:0000269 PubMed:24239382}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for KPTN

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with KPTN: view

No data available for Genatlas for KPTN Gene

Publications for KPTN Gene

  1. 2E4 (kaptin): a novel actin-associated protein from human blood platelets found in lamellipodia and the tips of the stereocilia of the inner ear. (PMID: 10099934) Bearer EL … Abraham MT (European journal of cell biology 1999) 2 3 4 22 58
  2. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. (PMID: 28199306) Wolfson RL … Sabatini DM (Nature 2017) 3 4 58
  3. Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures. (PMID: 24239382) Baple EL … Crosby AH (American journal of human genetics 2014) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for KPTN Gene

  • Addgene plasmids for KPTN

Sources for KPTN Gene

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