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Gene

NCSTN

nicastrin

Summary

Cytogenetic location
1q23.2
Coordinates
Chromosome 1: 160,343,383–160,358,949 (GRCh38)
Exons
17 exons across 15.6 kb
Protein
709 amino acids
Inheritance
Autosomal dominant
Also known as
KIAA0253, APH2
MANE Select transcript
ENST00000294785.10NM_015331.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Familial Hidradenitis Suppurativa

    • Autosomal dominant

      Hidradenitis suppurativa caused by variants in the gamma-secretase genes NCSTN, PSENEN or PSEN1, often with earlier onset and more extensive disease.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Earlier diagnosis supports earlier treatment, weight management and smoking cessation.

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How NCSTN is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 1, with a bracket where NCSTN sits. NCSTN and 27 genes near it on chromosome 1, from 159,851,166 to 160,851,165.Chromosome 11q23.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44160 Mb160.2 Mb160.4 Mb160.6 Mb160.8 Mb: 159,834,474–159,873,053, reverse strandVSIG8: 159,854,316–159,862,657, reverse strandVSIG8CFAP45: 159,872,364–159,900,165, reverse strandCFAP45TAGLN2: 159,918,106–159,925,546, reverse strandTAGLN2IGSF9: 159,927,039–159,949,468, reverse strandIGSF9SLAMF9: 159,951,492–159,954,237, reverse strandSLAMF9KCNJ10: 159,998,651–160,070,483, reverse strandKCNJ10PIGM: 160,024,953–160,031,990, reverse strandPIGMKCNJ9: 160,081,501–160,094,277, forward strandKCNJ9IGSF8: 160,091,340–160,101,109, reverse strandIGSF8ATP1A2: 160,115,755–160,143,605, forward strandATP1A2ATP1A4: 160,151,586–160,187,593, forward strandATP1A4CASQ1: 160,190,212–160,201,886, forward strandCASQ1PEA15: 160,205,328–160,220,335, forward strandPEA15DCAF8: 160,214,840–160,263,388, reverse strandDCAF8: 160,216,800–160,285,130, reverse strandPEX19: 160,266,229–160,286,348, reverse strandPEX19COPA: 160,288,580–160,343,566, reverse strandCOPANCSTN: 160,343,383–160,358,949, forward strandNCSTNNHLH1: 160,367,071–160,372,846, forward strandNHLH1VANGL2: 160,400,528–160,428,678, forward strandVANGL2SLAMF6: 160,484,817–160,523,273, reverse strandSLAMF6CD84: 160,541,095–160,579,544, reverse strandCD84SLAMF1: 160,608,100–160,647,056, reverse strandSLAMF1CD48: 160,678,746–160,711,831, reverse strandCD48SLAMF7: 160,739,057–160,754,821, forward strandSLAMF7LY9: 160,796,071–160,828,601, forward strandLY9CD244: 160,829,075–160,862,904, reverse strandCD244Diagram of NCSTN: 17 exons on the forward strand of chromosome 1Exon 3: 1 known disease-causing siteExon 4: 2 known disease-causing sitesExon 5: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 11: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 1: 160,343,383–160,343,481, 99 basesExon 2: 160,344,722–160,344,826, 105 basesExon 3: 160,348,999–160,349,122, 124 basesExon 4: 160,349,549–160,349,670, 122 basesExon 5: 160,350,105–160,350,250, 146 basesExon 6: 160,351,222–160,351,372, 151 basesExon 7: 160,351,696–160,351,805, 110 basesExon 8: 160,352,054–160,352,206, 153 basesExon 9: 160,352,887–160,352,991, 105 basesExon 10: 160,353,160–160,353,237, 78 basesExon 11: 160,354,118–160,354,290, 173 basesExon 12: 160,355,655–160,355,757, 103 basesExon 13: 160,355,863–160,355,958, 96 basesExon 14: 160,356,260–160,356,347, 88 basesExon 15: 160,356,600–160,356,754, 155 basesExon 16: 160,357,041–160,357,253, 213 basesExon 17: 160,358,149–160,358,949, 801 bases1246810121416175′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.8 kb of the gene's 15.6 kb; 2,130 of those bases code for the protein.

How a genome test reads NCSTN

8

positions in NCSTN where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 15.6 kb of NCSTN, introns included, not only the 2.8 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). NCSTN gene: nicastrin. Retrieved 17 October 2026, from https://dantelabs.com/genes/ncstn

Vancouver

Dante Labs. NCSTN gene: nicastrin [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ncstn

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