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Gene

CTSA

cathepsin A

Summary

Cytogenetic location
20q13.12
Coordinates
Chromosome 20: 45,891,335–45,898,820 (GRCh38)
Exons
15 exons across 7.5 kb
Protein
480 amino acids
Inheritance
Autosomal recessive
Previous symbols
GSL, PPGB
MANE Select transcript
ENST00000646241.3NM_000308.4
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

  • Alpha-Mannosidosis and Other Glycoproteinoses

    • GalactosialidosisAutosomal recessive

      Combined deficiency of neuraminidase and beta-galactosidase causing coarse features, cherry-red spots, myoclonus and organ enlargement, caused by CTSA variants.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

Broader groupings

  • Lysosomal Storage Disease

    • Lysosomal storage disease (other and unspecified types)

      One of 59 genes linked to it

      Covers lysosomal storage diseases without a dedicated report, such as Farber disease and other ASAH1-related disorders, prosaposin (PSAP) deficiencies, multiple sulfatase deficiency, mucopolysaccharidosis types IX and X, and Dorfman-Chanarin disease; inheritance varies by subtype, most often autosomal recessive.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CTSA is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 20, with a bracket where CTSA sits. CTSA and 36 genes near it on chromosome 20, from 45,395,078 to 46,395,077.Chromosome 2020q13.12p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3345.4 Mb45.6 Mb45.8 Mb46 Mb46.2 MbSYS1-DBNDD2: 45,363,200–45,410,610, forward strandSYS1-DBNDD2TP53TG5: 45,371,804–45,407,889, reverse strandTP53TG5DBNDD2: 45,405,616–45,410,870, forward strandDBNDD2PIGT: 45,416,084–45,456,934, forward strandPIGTWFDC2: 45,469,166–45,481,533, forward strandWFDC2SPINT3: 45,512,461–45,515,622, reverse strandWFDC6: 45,533,091–45,539,496, reverse strandWFDC6EPPIN-WFDC6: 45,534,196–45,547,662, reverse strandEPPIN-WFDC6EPPIN: 45,540,626–45,547,786, reverse strandEPPINWFDC8: 45,551,153–45,579,326, reverse strandWFDC8WFDC9: 45,607,939–45,631,284, reverse strandWFDC9WFDC10A: 45,629,733–45,631,196, forward strandWFDC10AWFDC11: 45,648,563–45,670,270, reverse strandWFDC11WFDC10B: 45,684,651–45,705,019, reverse strandWFDC10BWFDC13: 45,702,038–45,708,817, forward strandWFDC13SPINT4: 45,722,347–45,725,830, forward strandSPINT4WFDC3: 45,747,944–45,791,932, reverse strandWFDC3DNTTIP1: 45,791,937–45,811,427, forward strandDNTTIP1UBE2C: 45,812,561–45,816,965, forward strandUBE2CTNNC2: 45,823,214–45,833,745, reverse strandSNX21: 45,833,633–45,843,276, forward strandACOT8: 45,841,709–45,857,435, reverse strandZSWIM3: 45,857,591–45,879,131, forward strandZSWIM1: 45,881,201–45,885,266, forward strandSPATA25: 45,886,491–45,887,626, reverse strandSPATA25NEURL2: 45,888,002–45,891,220, reverse strandNEURL2CTSA: 45,891,335–45,898,820, forward strandCTSAPLTP: 45,897,535–45,912,235, reverse strandPLTPPCIF1: 45,934,673–45,948,023, forward strandZNF335: 45,948,653–45,972,358, reverse strandZNF335MMP9: 46,008,869–46,016,561, forward strandMMP9SLC12A5: 46,021,675–46,060,150, forward strandSLC12A5NCOA5: 46,060,984–46,089,973, reverse strandNCOA5CD40: 46,118,240–46,130,378, forward strandCD40CDH22: 46,173,737–46,309,009, reverse strandCDH22SLC35H1: 46,345,980–46,364,460, reverse strandSLC35H1ELMO2: 46,366,045–46,432,985, reverse strandELMO2Diagram of CTSA: 15 exons on the forward strand of chromosome 20Exon 2: 11 known disease-causing sitesExon 3: 5 known disease-causing sitesExon 4: 1 known disease-causing siteExon 5: 2 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 10: 2 known disease-causing sitesExon 11: 7 known disease-causing sitesExon 12: 3 known disease-causing sitesExon 13: 4 known disease-causing sitesExon 14: 4 known disease-causing sitesExon 1: 45,891,335–45,891,379, 45 basesExon 2: 45,891,569–45,891,762, 194 basesExon 3: 45,891,916–45,892,027, 112 basesExon 4: 45,892,273–45,892,323, 51 basesExon 5: 45,892,398–45,892,484, 87 basesExon 6: 45,892,725–45,892,880, 156 basesExon 7: 45,893,220–45,893,311, 92 basesExon 8: 45,893,988–45,894,072, 85 basesExon 9: 45,894,650–45,894,741, 92 basesExon 10: 45,894,823–45,894,901, 79 basesExon 11: 45,894,994–45,895,133, 140 basesExon 12: 45,896,965–45,897,040, 76 basesExon 13: 45,897,717–45,897,806, 90 basesExon 14: 45,898,005–45,898,109, 105 basesExon 15: 45,898,367–45,898,820, 454 bases1234567891011121314155′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 1.9 kb of the gene's 7.5 kb; 1,443 of those bases code for the protein.

How a genome test reads CTSA

68

positions in CTSA 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 7.5 kb of CTSA, introns included, not only the 1.9 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.). CTSA gene: cathepsin A. Retrieved 16 October 2026, from https://dantelabs.com/genes/ctsa

Vancouver

Dante Labs. CTSA gene: cathepsin A [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ctsa

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