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Gene

CST3

cystatin C

Summary

Cytogenetic location
20p11.21
Coordinates
Chromosome 20: 23,633,657–23,637,955 (GRCh38)
Exons
3 exons across 4.3 kb
Protein
146 amino acids
Inheritance
Autosomal dominant
MANE Select transcript
ENST00000376925.8NM_000099.4
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 reports relevant to this gene

  • Cerebral Amyloid Angiopathy

    • Autosomal dominant

      Hereditary cerebral hemorrhage with amyloidosis (HCHWA) describes a group of rare familial central nervous system disorders characterized by amyloid deposition in the cerebral blood vessels leading to hemorrhagic and non-hemorrhagic strokes, focal neurological deficits, and progressive cognitive decline eventually leading to dementia.

      • 1 GenCC submitter rates it definitive or strong

  • Hereditary Amyloidosis

    • Autosomal dominant

      Hereditary amyloidosis refers to a group of inherited conditions that make up one of the subtypes of amyloidosis. Hereditary amyloidosisis characterized by the deposit of an abnormal protein called amyloid in multiple organs of the body where it should not be, which causes disruption of organ tissue structure and function. In hereditary amyloidosis, amyloid deposits most often occur in tissues of the heart, kidneys, and nervous system. While symptoms of hereditary amyloidosis may appear in childhood, most individuals do not experience symptoms until adulthood. There are many types of hereditary amyloidosis associated with different gene mutations and abnormal proteins. The most common type of hereditary amyloidosis is transthyretin amyloidosis (ATTR), a condition in which the amyloid deposits are most often made up of the transthyretin protein which is made in the liver. Other examplesof hereditary amyloidosis include, but are not limited to, apolipoprotein AI amyloidosis (A ApoAI), gelsolin amyloidosis (A Gel), lysozyme amyloidosis (A Lys), cystatin C amyloidosis (A Cys), fibrinogen Aα-chain amyloidosis (A Fib), and apolipoprotein AII amyloidosis (A ApoAII).

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Tafamidis (kinetic stabilizer), patisiran (RNAi), vutrisiran (RNAi), inotersen (antisense), liver transplantation

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 CST3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 20, with a bracket where CST3 sits. CST3 and 13 genes near it on chromosome 20, from 23,135,806 to 24,135,805.Chromosome 2020p11.21p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3323.2 Mb23.4 Mb23.6 Mb23.8 Mb24 MbNXT1: 23,350,148–23,354,771, forward strandNXT1GZF1: 23,361,987–23,373,084, forward strandGZF1NAPB: 23,371,267–23,421,520, reverse strandNAPBCSTL1: 23,426,104–23,444,930, forward strandCSTL1CST11: 23,450,403–23,453,210, reverse strandCST11CST8: 23,491,101–23,496,010, forward strandCST8CST9L: 23,564,731–23,568,517, reverse strandCST9LCST9: 23,602,410–23,605,917, reverse strandCST9CST3: 23,633,657–23,637,955, reverse strandCST3CST4: 23,685,640–23,689,038, reverse strandCST4CST1: 23,747,560–23,751,268, reverse strandCST1CST2: 23,823,769–23,826,735, reverse strandCST2CST5: 23,875,934–23,880,086, reverse strandCST5GGTLC1: 23,985,050–23,988,779, reverse strandGGTLC1Diagram of CST3: 3 exons on the reverse strand of chromosome 20Exon 3: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 3: 23,633,657–23,633,999, 343 basesExon 2: 23,635,254–23,635,367, 114 basesExon 1: 23,637,620–23,637,955, 336 bases3215′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 0.8 kb of the gene's 4.3 kb; 441 of those bases code for the protein.

How a genome test reads CST3

2

positions in CST3 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 4.3 kb of CST3, introns included, not only the 0.8 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.). CST3 gene: cystatin C. Retrieved 17 October 2026, from https://dantelabs.com/genes/cst3

Vancouver

Dante Labs. CST3 gene: cystatin C [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cst3

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