What you carry at this position in your DNA and what research says about it.
Gut and Liver Inflammation: 10/10 evidence, 33 publications.
You're viewing every possible genotype for this variant.
None of these is your result. Use the genotype toggle to compare them, then sign up and upload your DNA to see which one is yours.
Sample genotype (not yours): G/G
Typical Risk of Gut and Liver Inflammation
Inheriting two copies of the common G allele is associated with typical, baseline risk for inflammatory bowel diseases and related liver conditions. This genotype maintains normal levels of macrophage-stimulating protein, helping regulate healthy immune responses.
What this genotype means: Typical risk of Crohns disease; Typical risk of ulcerative colitis; Typical risk of primary sclerosing cholangitis.
Sample genotype (not yours): A/A
Increased Risk of Gut and Liver Inflammation
Inheriting two copies of the A allele is associated with an increased risk of inflammatory bowel diseases and primary sclerosing cholangitis. This genotype significantly lowers levels of macrophage-stimulating protein, which can promote chronic inflammation in the gut and bile ducts.
What this genotype means: Increased risk of Crohns disease; Increased risk of ulcerative colitis; Increased risk of primary sclerosing cholangitis.
Sample genotype (not yours): G/A
Slightly Increased Risk of Gut and Liver Inflammation
Carrying one copy of the A allele is associated with a slightly elevated risk of inflammatory bowel diseases and primary sclerosing cholangitis. This genetic variation slightly alters immune cell signaling, which can lead to a more active inflammatory response in the digestive tract.
What this genotype means: Slightly increased risk of Crohns disease; Slightly increased risk of ulcerative colitis; Slightly increased risk of primary sclerosing cholangitis.
Gene function and biological role
Gene Function: The APEH gene encodes acylaminoacyl-peptide hydrolase, an enzyme that plays a key role in clearing damaged or modified proteins from cells. It is located on chromosome 3 in close proximity to the MST1 gene, which encodes macrophage-stimulating protein [1]. While APEH is vital for cellular protein recycling, many genetic studies in this specific region highlight its neighbor, MST1, as a major player in immune system regulation [2]. Macrophage-stimulating protein is crucial for controlling inflammatory responses, cell migration, and tissue repair in the gut and liver [2]. Consequently, genetic variations in this chromosomal neighborhood are heavily studied for their impact on chronic inflammatory disorders [2].
Variant Impact: The rs3197999 variant is a missense mutation that alters the structure of the macrophage-stimulating protein encoded by the neighboring MST1 gene [1]. This specific amino acid change affects how the protein interacts with immune cells, particularly macrophages, altering their activation and movement [1]. Research indicates that this genetic change leads to a functional alteration in how the body regulates inflammation in the digestive tract and bile ducts [1] [2]. Because of this direct impact on immune signaling, the variant is one of the most strongly replicated genetic markers for susceptibility to inflammatory bowel diseases and related liver conditions [2].
Key Insight: This variant is one of the top genetic markers linking inflammatory bowel disease directly to primary sclerosing cholangitis, a rare progressive liver disease.
Location: MST1. Chromosome 3 · 3p21.31 · 49.7 Mb
Estimated prevalence by population
Global 54.7%; European 51.2%; African 59.1%; East Asian 91.2%; South Asian 62.5%; Americas 63.6%; Ashkenazi 31.1%; Finnish 33.2%; Middle Eastern 48.6%; Amish 64.4%.
Estimated GG genotype frequency.
Global 37.8%; European 40.7%; African 35.6%; East Asian 8.6%; South Asian 33.1%; Americas 32.3%; Ashkenazi 49.3%; Finnish 48.8%; Middle Eastern 42.2%; Amish 31.7%.
Estimated GA genotype frequency.
Global 7.5%; European 8.1%; African 5.4%; East Asian 0.2%; South Asian 4.4%; Americas 4.1%; Ashkenazi 19.6%; Finnish 18.0%; Middle Eastern 9.2%; Amish 3.9%.
Estimated AA genotype frequency.
Showing effects for G/G genotype
Immunity & Inflammation
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 7/10. Source: PMID 18587394. Typical Risk.
Ulcerative Colitis. Evidence: 8/10. Source: PMID 20228799. Typical Risk.
Inflammatory Bowel Disease. Evidence: 8/10. Source: PMID 23128233. Typical Risk.
Inflammatory & Circulating Protein Markers
MSP Protein Levels. Evidence: 7/10. Source: PMID 36168886. Higher Levels.
Organ Systems
Liver Function & Disease
Sclerosing Cholangitis. Evidence: 10/10. Source: PMID 21151127. Typical Risk.
Showing effects for A/A genotype
Crohn's Disease. Evidence: 7/10. Source: PMID 18587394. ~1.2x Risk.
Ulcerative Colitis. Evidence: 8/10. Source: PMID 20228799. ~1.19x Risk.
Inflammatory Bowel Disease. Evidence: 8/10. Source: PMID 23128233. ~1.18x Risk.
MSP Protein Levels. Evidence: 7/10. Source: PMID 36168886. Lower Levels.
Sclerosing Cholangitis. Evidence: 10/10. Source: PMID 21151127. ~1.33x Risk.
Showing effects for G/A genotype
Crohn's Disease. Evidence: 7/10. Source: PMID 18587394. Slightly Increased.
Ulcerative Colitis. Evidence: 8/10. Source: PMID 20228799. Slightly Increased.
Inflammatory Bowel Disease. Evidence: 8/10. Source: PMID 23128233. Slightly Increased.
MSP Protein Levels. Evidence: 7/10. Source: PMID 36168886. Intermediate.
Sclerosing Cholangitis. Evidence: 10/10. Source: PMID 21151127. Slightly Increased.
What this genotype means for the people who carry it
Sample genotype: GG (Homozygous)
Maintaining normal immune regulation in the digestive tract is heavily influenced by the G/G genotype. Large-scale genetic studies show that this genotype is protective against the elevated risks of Crohns disease and ulcerative colitis seen in carriers of the A allele [1]. It is also associated with a typical, baseline risk for primary sclerosing cholangitis, a rare inflammatory condition of the bile ducts [2]. The biological mechanism involves maintaining standard levels of macrophage-stimulating protein, which prevents the over-activation of inflammatory pathways in the gut and liver [3]. While having this genotype does not make someone immune to inflammatory diseases, it means they do not carry the genetic risk elevation associated with this specific locus [1] [2].
Typical risk of Crohns disease; Typical risk of ulcerative colitis; Typical risk of primary sclerosing cholangitis.
Sample genotype: AA (Homozygous)
Two copies of the A allele are associated with the highest genetic risk at this locus for chronic inflammatory conditions. Multiple large-scale studies have confirmed that this genotype increases the risk of Crohns disease and ulcerative colitis by approximately 1.2-fold [1]. Additionally, it is associated with a 1.33-fold increased risk of primary sclerosing cholangitis, a progressive inflammatory disease of the livers bile ducts [2]. The underlying biology shows that this genotype leads to significantly reduced levels of macrophage-stimulating protein, impairing the bodys ability to resolve inflammation in mucosal tissues [3]. While this genetic profile increases susceptibility, it is not a direct diagnosis, and many individuals with this genotype never develop these conditions.
Increased risk of Crohns disease; Increased risk of ulcerative colitis; Increased risk of primary sclerosing cholangitis.
Sample genotype: GA (Heterozygous)
A single copy of the A allele introduces a subtle shift in the bodys inflammatory baseline. Genome-wide association studies have consistently linked this heterozygous state to a modest increase in the risk of developing Crohns disease and ulcerative colitis [1]. There is also a slightly higher susceptibility to primary sclerosing cholangitis, an inflammatory liver condition that often co-occurs with inflammatory bowel disease [2]. The genetic change leads to slightly lower circulating levels of macrophage-stimulating protein, which can alter how macrophages respond to gut microbes and trigger inflammation [3]. Although the absolute risk remains low for most people, maintaining a healthy gut microbiome and discussing any persistent digestive symptoms with a healthcare provider can be helpful.
Slightly increased risk of Crohns disease; Slightly increased risk of ulcerative colitis; Slightly increased risk of primary sclerosing cholangitis.
Variants with shared genetic architecture
rs10761659 · ZNF365 Gene · Chr 10 · Crohn's Disease Risk
rs17293632 · SMAD3 Gene · Chr 15 · Inflammatory Disease Risk
rs7554511 · INAVA Gene · Chr 1 · Inflammatory Bowel Disease
Content updated August 2026.
ReadYourDNA provides educational interpretation of DNA data you already have. It is not diagnostic, not a substitute for professional medical advice, diagnosis, or treatment, and is not intended to diagnose, treat, cure, or prevent any disease. Talk to a clinician before acting on any result.
Raw DNA Data Reports for 23andMe & AncestryDNA · About ReadYourDNA · FAQ · Methodology & Science · Pricing · Support and complaints · Legal & Contact · Health Traits · Pharmacogenomics · Carrier Status · Variant Explorer · The Human Karyotype · Privacy Policy · Terms of Service · Accessibility · Consumer Health Data Privacy · Your Privacy Choices · Editorial Standards · Your Data, Checkable · Sample Report · ReadYourDNA and Promethease compared · What is inside a 23andMe raw data file · What is inside an AncestryDNA raw data file · What a chatbot can and cannot do with your raw DNA file · Where a raw DNA file can still be uploaded in 2026
Written, maintained and operated by Martin Pechhacker, sole proprietor, Vienna, Austria. Trade register GISA 40064420. support@readyourdna.com