Genetic landscape of ALPL and other genes impacting alkaline phosphatase variation in the UK Biobank
Biochemical/Metabolic and Therapeutics
-
Primary Categories:
- Basic Research
-
Secondary Categories:
- Basic Research
Introduction:
Hypophosphatasia (HPP) is a rare, inherited metabolic disorder caused by low tissue non-specific alkaline phosphatase (ALP) activity. Tissue non-specific ALP is a cell-surface phosphohydrolase expressed in bone, kidney and liver and is encoded by the ALPL gene. Deficient ALP activity can lead to extra-cellular accumulation of substrates like inorganic pyrophosphate (PPi) and pyridoxal 5-phosphate (PLP), which can interfere with bone mineralization and other physiological processes. We analyzed the prevalence and impact on ALP levels of genetic variants in ALPL and other genes in the UK Biobank (UKB), a large-scale population study, to elucidate the genetic underpinnings of ALP levels and HPP.
Methods:
We examined whole-genome sequencing (WGS) and ALP data from the UKB, focusing primarily on subjects positive for known pathogenic variants in the ALPL gene (identified from public data sources such as ClinVar and the JKU ALPL Gene Variant Database). Subjects carrying pathogenic variants were analyzed to identify variant contribution to measured ALP levels. Exome-wide association studies (exWAS) and collapsing analyses (Wang et al, 2021) were performed on the UKB cohort to identify additional genetic contributors to ALP levels.
Results:
2,800 subjects out of 484,110 UKB participants with WGS data passing QC filters (0.6%) had at least one pathogenic ALPL variant, the most common genotype being c.571G>A in the heterozygous state (618 subjects). We identified 12 individuals with compound heterozygous variants and one with a homozygous c.571G>A variant. It was not possible to determine whether compound heterozygotes were biallelic due to lack of phase information.
Our analysis confirmed a strong association between the presence of pathogenic ALPL variants and persistently low ALP levels, defined as average ALP <= 40 IU/L (OR=185.6, Fisher p-value < 2.2e-16) across two measurements. No measurements of ALP substrates such as PPi or PLP were available. However, the effect of ALPL genetic variation on average ALP levels was unequal. Fourteen c.571G>A heterozygotes had multiple ALP measurements, but only 2 of them had persistently low ALP (14.3%). Given that persistently low ALP is a hallmark of HPP, this suggests low HPP penetrance of variant c.571G>A and contradicts previously reported 50% penetrance of heterozygous hypomorphic ALPL variants (Mornet et al., 2021). Persistently low ALP was observed more frequently in individuals heterozygous for other pathogenic ALPL variants (35 of 88 cases, 39.8%). Persistently low ALP was also observed in 50 out of 16,506 individuals (0.3%) without any pathogenic ALPL variant, highlighting the potential contribution of other genetic or environmental factors in ALP levels. ExWAS and collapsing analyses identified 12 genome-wide significant genes beyond ALPL affecting ALP levels (p-value cutoff: 1e-8). Variants in genes GPLD1, IFITM5, APOB, PCK1 and HSPG2 were associated with a decrease in average ALP levels, while variants in ABCB11, ASGR1, EDEM1, AKAP9, SLC39A5 and B4GALNT3 were associated with increased ALP levels. These findings demonstrate that rare, high-impact variants in genes other than ALPL can bi-directionally influence ALP levels.
Conclusion:
Our UK Biobank analyses reinforce the strong association of pathogenic ALPL variants and persistently low ALP levels. However, the HPP penetrance of heterozygous hypomorphic ALPL variants, particularly c.571G>A, may be lower than previously reported. This observed lower penetrance may explain why the highly prevalent c.571G>A heterozygous genotype has low frequency in HPP patient cohorts, such as the Global HPP Registry (4.4% of subjects, Kishnani et al, 2024). Our rare variant analyses identified additional genetic contributors to ALP levels, expanding on prior common variant analyses, and underscore the polygenic nature of ALP regulation. Future studies should aim to refine HPP penetrance estimates for pathogenic ALPL variants, and to elucidate the contributions of non-ALPL variants to persistently low ALP and HPP.
Hypophosphatasia (HPP) is a rare, inherited metabolic disorder caused by low tissue non-specific alkaline phosphatase (ALP) activity. Tissue non-specific ALP is a cell-surface phosphohydrolase expressed in bone, kidney and liver and is encoded by the ALPL gene. Deficient ALP activity can lead to extra-cellular accumulation of substrates like inorganic pyrophosphate (PPi) and pyridoxal 5-phosphate (PLP), which can interfere with bone mineralization and other physiological processes. We analyzed the prevalence and impact on ALP levels of genetic variants in ALPL and other genes in the UK Biobank (UKB), a large-scale population study, to elucidate the genetic underpinnings of ALP levels and HPP.
Methods:
We examined whole-genome sequencing (WGS) and ALP data from the UKB, focusing primarily on subjects positive for known pathogenic variants in the ALPL gene (identified from public data sources such as ClinVar and the JKU ALPL Gene Variant Database). Subjects carrying pathogenic variants were analyzed to identify variant contribution to measured ALP levels. Exome-wide association studies (exWAS) and collapsing analyses (Wang et al, 2021) were performed on the UKB cohort to identify additional genetic contributors to ALP levels.
Results:
2,800 subjects out of 484,110 UKB participants with WGS data passing QC filters (0.6%) had at least one pathogenic ALPL variant, the most common genotype being c.571G>A in the heterozygous state (618 subjects). We identified 12 individuals with compound heterozygous variants and one with a homozygous c.571G>A variant. It was not possible to determine whether compound heterozygotes were biallelic due to lack of phase information.
Our analysis confirmed a strong association between the presence of pathogenic ALPL variants and persistently low ALP levels, defined as average ALP <= 40 IU/L (OR=185.6, Fisher p-value < 2.2e-16) across two measurements. No measurements of ALP substrates such as PPi or PLP were available. However, the effect of ALPL genetic variation on average ALP levels was unequal. Fourteen c.571G>A heterozygotes had multiple ALP measurements, but only 2 of them had persistently low ALP (14.3%). Given that persistently low ALP is a hallmark of HPP, this suggests low HPP penetrance of variant c.571G>A and contradicts previously reported 50% penetrance of heterozygous hypomorphic ALPL variants (Mornet et al., 2021). Persistently low ALP was observed more frequently in individuals heterozygous for other pathogenic ALPL variants (35 of 88 cases, 39.8%). Persistently low ALP was also observed in 50 out of 16,506 individuals (0.3%) without any pathogenic ALPL variant, highlighting the potential contribution of other genetic or environmental factors in ALP levels. ExWAS and collapsing analyses identified 12 genome-wide significant genes beyond ALPL affecting ALP levels (p-value cutoff: 1e-8). Variants in genes GPLD1, IFITM5, APOB, PCK1 and HSPG2 were associated with a decrease in average ALP levels, while variants in ABCB11, ASGR1, EDEM1, AKAP9, SLC39A5 and B4GALNT3 were associated with increased ALP levels. These findings demonstrate that rare, high-impact variants in genes other than ALPL can bi-directionally influence ALP levels.
Conclusion:
Our UK Biobank analyses reinforce the strong association of pathogenic ALPL variants and persistently low ALP levels. However, the HPP penetrance of heterozygous hypomorphic ALPL variants, particularly c.571G>A, may be lower than previously reported. This observed lower penetrance may explain why the highly prevalent c.571G>A heterozygous genotype has low frequency in HPP patient cohorts, such as the Global HPP Registry (4.4% of subjects, Kishnani et al, 2024). Our rare variant analyses identified additional genetic contributors to ALP levels, expanding on prior common variant analyses, and underscore the polygenic nature of ALP regulation. Future studies should aim to refine HPP penetrance estimates for pathogenic ALPL variants, and to elucidate the contributions of non-ALPL variants to persistently low ALP and HPP.