Gene
CTNNA1
catenin alpha 1
- HGNC 2509(opens in a new tab)
- Ensembl gene ENSG00000044115(opens in a new tab)
- NCBI Gene 1495(opens in a new tab)
Summary
- Cytogenetic location
- 5q31.2
- Coordinates
- Chromosome 5: 138,753,425–138,935,034 (GRCh38)
- Exons
- 18 exons across 181.6 kb
- Protein
- 906 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- CAP102
- MANE Select transcript
- ENST00000302763.12NM_001903.5
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Get my Genome TestCurated reports relevant to this gene
Hereditary Diffuse Gastric Cancer
- CTNNA1-related diffuse gastric and lobular breast cancer syndromeAutosomal dominant
CTNNA1 variants that raise the risk of diffuse gastric cancer and lobular breast cancer.
- ClinGen rates the link definitive
- 1 GenCC submitter rates it definitive or strong
What knowing changes
Endoscopic surveillance and breast screening are usually advised.
Breast and Ovarian Cancer Genes Beyond BRCA1/2
- Hereditary breast cancerAutosomal dominant
Inherited susceptibility to breast cancer caused by variants in one of several genes.
- ClinGen rates the link definitive
- 1 GenCC submitter rates it definitive or strong
What knowing changes
Earlier and more intensive breast screening, including MRI, may be recommended depending on the gene.
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 CTNNA1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 3.8 kb of the gene's 181.6 kb; 2,721 of those bases code for the protein.
How a genome test reads CTNNA1
100
positions in CTNNA1 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 181.6 kb of CTNNA1, introns included, not only the 3.8 kb of exons.
Traits linked to CTNNA1
The Human Phenotype Ontology lists these as features of the rare conditions CTNNA1 can cause. Each trait's page lists the other genes linked to it.
External links
Gene records
Transcript
Protein
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
Dante Labs. (n.d.). CTNNA1 gene: catenin alpha 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/ctnna1
Dante Labs. CTNNA1 gene: catenin alpha 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ctnna1
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