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    NCSTN nicastrin [ Homo sapiens (human) ]

    Gene ID: 23385, updated on 27-Dec-2024

    Summary

    Official Symbol
    NCSTNprovided by HGNC
    Official Full Name
    nicastrinprovided by HGNC
    Primary source
    HGNC:HGNC:17091
    See related
    Ensembl:ENSG00000162736 MIM:605254; AllianceGenome:HGNC:17091
    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
    ATAG1874
    Summary
    This gene encodes a type I transmembrane glycoprotein that is an integral component of the multimeric gamma-secretase complex. The encoded protein cleaves integral membrane proteins, including Notch receptors and beta-amyloid precursor protein, and may be a stabilizing cofactor required for gamma-secretase complex assembly. The cleavage of beta-amyloid precursor protein yields amyloid beta peptide, the main component of the neuritic plaque and the hallmark lesion in the brains of patients with Alzheimer's disease; however, the nature of the encoded protein's role in Alzheimer's disease is not known for certain. Mutations in this gene are associated with familial acne inversa. A pseudogene of this gene is present on chromosome 21. Alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Feb 2014]
    Expression
    Ubiquitous expression in placenta (RPKM 38.1), duodenum (RPKM 30.4) and 25 other tissues See more
    Orthologs
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    Genomic context

    See NCSTN in Genome Data Viewer
    Location:
    1q23.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160343383..160358949)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159480455..159496021)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160313173..160328739)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985219 Neighboring gene peroxisomal biogenesis factor 19 Neighboring gene COPI coat complex subunit alpha Neighboring gene SUMO1 pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:160312973-160313920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1921 Neighboring gene uncharacterized LOC105371466 Neighboring gene nescient helix-loop-helix 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1922 Neighboring gene RNA, U4 small nuclear 42, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Clone Names

    • KIAA0253, RP11-517F10.1

    Gene Ontology Provided by GOA

    Items 1 - 25 of 39
    Process Evidence Code Pubs
    involved_in G protein-coupled dopamine receptor signaling pathway  
    involved_in Notch receptor processing  
    involved_in Notch receptor processing PubMed 
    involved_in Notch receptor processing PubMed 
    involved_in Notch receptor processing PubMed 
    involved_in Notch receptor processing PubMed 
    involved_in Notch signaling pathway  
    involved_in T cell proliferation  
    involved_in adult behavior  
    involved_in amyloid precursor protein biosynthetic process  
    involved_in amyloid precursor protein catabolic process PubMed 
    involved_in amyloid precursor protein catabolic process PubMed 
    involved_in amyloid precursor protein catabolic process  
    involved_in amyloid precursor protein catabolic process PubMed 
    involved_in amyloid precursor protein metabolic process PubMed 
    involved_in amyloid-beta formation PubMed 
    involved_in amyloid-beta formation PubMed 
    involved_in amyloid-beta formation PubMed 
    involved_in cellular response to calcium ion  
    involved_in central nervous system myelination  
    involved_in cerebellum development  
    involved_in epithelial cell proliferation  
    involved_in glutamate receptor signaling pathway  
    involved_in learning or memory  
    involved_in membrane protein ectodomain proteolysis PubMed 
    involved_in membrane protein intracellular domain proteolysis PubMed 
    involved_in membrane protein intracellular domain proteolysis  
    involved_in myeloid cell homeostasis  
    involved_in neuron apoptotic process  
    involved_in positive regulation of amyloid precursor protein biosynthetic process  
    involved_in positive regulation of endopeptidase activity PubMed 
    involved_in positive regulation of endopeptidase activity PubMed 
    involved_in protein processing  
    involved_in protein processing PubMed 
    involved_in protein processing PubMed 
    involved_in protein processing PubMed 
    involved_in proteolysis PubMed 
    involved_in regulation of long-term synaptic potentiation  
    involved_in short-term synaptic potentiation  
    Items 1 - 25 of 39
    Items 1 - 20 of 26
    Component Evidence Code Pubs
    located_in Golgi apparatus PubMed 
    located_in Golgi membrane PubMed 
    located_in azurophil granule membrane  
    located_in early endosome  
    located_in endoplasmic reticulum PubMed 
    located_in endoplasmic reticulum membrane PubMed 
    located_in endosome membrane  
    located_in extracellular exosome PubMed 
    located_in focal adhesion PubMed 
    part_of gamma-secretase complex PubMed 
    part_of gamma-secretase complex PubMed 
    part_of gamma-secretase complex PubMed 
    part_of gamma-secretase complex  
    part_of gamma-secretase complex PubMed 
    located_in lysosomal membrane PubMed 
    located_in melanosome  
    located_in membrane PubMed 
    located_in membrane PubMed 
    located_in membrane PubMed 
    is_active_in plasma membrane  
    located_in plasma membrane PubMed 
    located_in plasma membrane  
    located_in plasma membrane  
    located_in presynaptic membrane  
    located_in sarcolemma  
    located_in synaptic vesicle  
    Items 1 - 20 of 26

    General protein information

    Preferred Names
    nicastrin
    Names
    anterior pharynx-defective 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.

    Genomic

    1. NG_027935.1 RefSeqGene

      Range
      5111..20677
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_223

    mRNA and Protein(s)

    1. NM_001290184.2 → NP_001277113.1  nicastrin isoform 2

      See identical proteins and their annotated locations for NP_001277113.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has a different 5' structure resulting in translation initiation at an alternate AUG compared to variant 1; the 5'-most AUG, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the alternate AUG resulting in a shorter isoform (2) with a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AL445230, BC047621, CN429672
      UniProtKB/TrEMBL
      A0A8V8TNI3
      Conserved Domains (1) summary
      cd03881
      Location:155 → 462
      M28_Nicastrin; M28 Zn-Peptidase Nicastrin, a main component of gamma-secretase complex
    2. NM_001290186.2 → NP_001277115.1  nicastrin isoform 3 precursor

      See identical proteins and their annotated locations for NP_001277115.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate in-frame exons in the coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AF240468, AK299142, AL445230, CN429672
      Consensus CDS
      CCDS91084.1
      UniProtKB/TrEMBL
      A0A8V8TPR8, B4DR82
      Related
      ENSP00000514429.1, ENST00000699549.1
      Conserved Domains (1) summary
      cl14876
      Location:195 → 361
      Zinc_peptidase_like; Zinc peptidases M18, M20, M28, and M42
    3. NM_001349729.2 → NP_001336658.1  nicastrin isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 5, which is shorter than isoform 1.
      Source sequence(s)
      AL445230, H15133
      UniProtKB/TrEMBL
      A0A8V8TNI3
      Related
      ENSP00000514420.1, ENST00000699528.1
      Conserved Domains (1) summary
      cd03881
      Location:175 → 482
      M28_Nicastrin; M28 Zn-Peptidase Nicastrin, a main component of gamma-secretase complex
    4. NM_015331.3 → NP_056146.1  nicastrin isoform 1 precursor

      See identical proteins and their annotated locations for NP_056146.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF240468, BC047621, CN429672
      Consensus CDS
      CCDS1203.1
      UniProtKB/Swiss-Prot
      Q5T207, Q5T208, Q86VV5, Q92542
      UniProtKB/TrEMBL
      A0A8V8TNI3
      Related
      ENSP00000294785.5, ENST00000294785.10
      Conserved Domains (1) summary
      cd03881
      Location:52 → 654
      M28_Nicastrin; M28 Zn-peptidase nicastrin, a main component of gamma-secretase complex

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      160343383..160358949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005245053.6 → XP_005245110.1  nicastrin isoform X1

      UniProtKB/TrEMBL
      A0A8V8TNC8, A0A8V8TPQ8
      Related
      ENSP00000514419.1, ENST00000699527.1
      Conserved Domains (1) summary
      cd03881
      Location:175 → 395
      M28_Nicastrin; M28 Zn-Peptidase Nicastrin, a main component of gamma-secretase complex

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      159480455..159496021
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335628.1 → XP_054191603.1  nicastrin isoform X1

      UniProtKB/TrEMBL
      A0A8V8TNC8, A0A8V8TPQ8
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