What you carry at this position in your DNA and what research says about it.
Bone and Tooth Health: 10/10 evidence, 10 publications.
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Sample genotype (not yours): G/G
Typical Bone and Tooth Health
Two copies of the typical G allele are associated with normal alkaline phosphatase activity and healthy bone mineralization. There is no elevated risk of hypophosphatasia or related skeletal and dental issues.
What this genotype means: Normal bone mineralization; Typical alkaline phosphatase levels.
Sample genotype (not yours): A/A
High Risk of Hypophosphatasia
A significant deficiency in alkaline phosphatase occurs with two copies of the A allele, leading to hypophosphatasia. This rare metabolic condition is characterized by defective bone mineralization, frequent fractures, and severe dental complications.
What this genotype means: Severe alkaline phosphatase deficiency; Defective bone and tooth mineralization; Frequent bone fractures and pain.
Sample genotype (not yours): G/A
Increased Risk of Bone and Tooth Weakness
Lower alkaline phosphatase levels and mild bone or dental issues can occur with one copy of the A allele. While often asymptomatic, some carriers experience adult-onset joint pain, slow-healing fractures, or early tooth loss.
What this genotype means: Lower alkaline phosphatase levels; Possible early tooth loss; Increased susceptibility to stress fractures.
Gene function and biological role
Gene Function: The ALPL gene encodes tissue-nonspecific alkaline phosphatase, an enzyme essential for proper bone and tooth mineralization [1]. This enzyme breaks down compounds like inorganic pyrophosphate, which otherwise inhibit the crystallization of calcium and phosphate in bones [2]. Without sufficient enzyme activity, minerals cannot deposit correctly, leading to skeletal weakness and dental complications [1]. The gene is highly active in osteoblasts and odontoblasts during development and throughout adulthood [2].
Variant Impact: A missense mutation in the ALPL gene, rs121918007 results in the substitution of the amino acid glutamic acid with lysine at position 191 of the protein [1]. This specific change, historically referred to as E174K, significantly reduces the enzymatic activity of alkaline phosphatase [1] [2]. It is considered one of the most common mutations causing hypophosphatasia in populations of European ancestry [1]. Because it arose from a single ancestral founder in northwestern Europe, it is particularly prevalent in people of European descent [1].
Key Insight: A single copy of this variant can cause mild bone and dental symptoms in adulthood, making it a frequently underdiagnosed cause of early tooth loss and unexplained fractures.
Location: ALPL. Chromosome 1 · 1p36.12 · 21.6 Mb
Estimated prevalence by population
Global 99.6%; European 99.7%; African 100.0%; East Asian 100.0%; South Asian > 99.9%; Americas 99.9%; Ashkenazi 100.0%; Finnish 96.6%; Middle Eastern 100.0%; Amish 100.0%.
Estimated GG genotype frequency.
Global 0.4%; European 0.3%; African 0.0%; East Asian 0.0%; South Asian < 0.1%; Americas 0.1%; Ashkenazi 0.0%; Finnish 3.3%; Middle Eastern 0.0%; Amish 0.0%.
Estimated GA genotype frequency.
Global < 0.1%; European < 0.1%; African 0.0%; East Asian 0.0%; South Asian < 0.1%; Americas < 0.1%; Ashkenazi 0.0%; Finnish < 0.1%; Middle Eastern 0.0%; Amish 0.0%.
Estimated AA genotype frequency.
Showing effects for G/G genotype
Organ Systems
Bone, Joint & Connective Tissue Health
Bone Mineralization. Evidence: 7/10. Source: PMID 12357339. Typical.
Liver Function & Disease
Alkaline Phosphatase. Evidence: 10/10. Source: PMID 33462484. Typical.
Nutrition & Metabolism
Blood Chemistry & Metabolites
Choline Phosphate Levels. Evidence: 5/10. Source: PMID 35347128. Typical.
Showing effects for A/A genotype
Bone Mineralization. Evidence: 7/10. Source: PMID 12357339. Severely Impaired.
Alkaline Phosphatase. Evidence: 10/10. Source: PMID 33462484. Very Low Levels.
Choline Phosphate Levels. Evidence: 5/10. Source: PMID 35347128. Very High Levels.
Showing effects for G/A genotype
Bone Mineralization. Evidence: 7/10. Source: PMID 12357339. Mildly Impaired.
Alkaline Phosphatase. Evidence: 10/10. Source: PMID 33462484. Lower Levels.
Choline Phosphate Levels. Evidence: 5/10. Source: PMID 35347128. Higher Levels.
What this genotype means for the people who carry it
Sample genotype: GG (Homozygous)
Maintaining two copies of the common G allele ensures that the tissue-nonspecific alkaline phosphatase enzyme functions at normal levels [1]. This normal enzymatic activity is crucial for the proper deposition of calcium and phosphate into bones and teeth, preventing skeletal softening [1] [2]. Individuals with this genotype typically exhibit standard blood levels of alkaline phosphatase and do not accumulate excess substrates like choline phosphate [3]. Consequently, there is no genetic predisposition to the bone fractures, early tooth loss, or joint pain associated with hypophosphatasia [1] [4]. Standard dental and bone health practices are sufficient to maintain skeletal integrity.
Normal bone mineralization; Typical alkaline phosphatase levels.
Sample genotype: AA (Homozygous)
A severe deficiency in functional tissue-nonspecific alkaline phosphatase results from inheriting two copies of the A allele [1] [2]. This profound lack of enzyme activity prevents calcium and phosphate from properly crystallizing in the skeleton, resulting in hypophosphatasia [1] [3]. Affected individuals often experience childhood or adult-onset symptoms, including soft bones, frequent fractures, bone pain, and premature loss of teeth with intact roots [3] [4]. Laboratory findings typically show extremely low serum alkaline phosphatase levels alongside elevated levels of choline phosphate and other metabolites [5]. Management of this condition usually involves specialized medical care, bone-targeted therapies, and close dental monitoring [6].
Severe alkaline phosphatase deficiency; Defective bone and tooth mineralization; Frequent bone fractures and pain.
Sample genotype: GA (Heterozygous)
Reduction in the overall activity of the alkaline phosphatase enzyme occurs when one copy of the A allele is present, which can impair the body's ability to mineralize bones and teeth [1] [2]. Although many carriers remain healthy and asymptomatic, this genotype is associated with mild, adult-onset forms of hypophosphatasia [3]. Symptoms can vary widely even within the same family, ranging from premature loss of baby teeth to recurrent stress fractures and chronic joint pain [4]. Blood tests typically reveal lower-than-average alkaline phosphatase levels, and some individuals may show elevated levels of metabolites like choline phosphate [5]. Discussing these findings with a healthcare provider can help monitor bone density and dental health proactively.
Lower alkaline phosphatase levels; Possible early tooth loss; Increased susceptibility to stress fractures.
Variants with shared genetic architecture
rs4654748 · NBPF3 Gene · Chr 1 · Vitamin B6 Levels
rs8736 · MBOAT7 Gene · Chr 19 · Fatty Liver Disease Risk
rs12188300 · IL12B Gene · Chr 5 · Psoriasis Risk
Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci.
Unexpected high intrafamilial phenotypic variability observed in hypophosphatasia.
Parathyroid hormone treatment improves pain and fracture healing in adult hypophosphatasia.
Content updated August 2026.
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