ClinVar Genomic variation as it relates to human health

The ALPL c.407G>A; p.Arg136His variant (rs121918011), also known as R119H, is reported in the literature in multiple individuals affected with hypophosphatasia, including many individuals who have another pathogenic variant on the opposite chromosome (Brun-Heath 2005, Cui 2012, Mumm 2002, Taillandier 1999, Taillandier 2001, Taillandier 2018, Taketani 2014, Whyte 2012, Whyte 2015). This variant is reported in ClinVar (Variation ID: 13675), and is found in the general population with an overall allele frequency of 0.013% (36/282262 alleles) in the Genome Aggregation Database. The arginine at codon 136 is moderately conserved, and computational analyses (SIFT: tolerated, PolyPhen-2: probably damaging) predict conflicting effects of this variant on protein structure/function. However, in vitro functional analyses demonstrate a significant reduction in protein activity (Fauvert 2009). Additionally, other amino acid substitutions at this codon (Cys, Leu, Pro) have been reported in individuals with hypophosphatasia (Cui 2012, Taillandier 2018, Yang 2013). Based on available information, this variant is considered to be pathogenic. References: Brun-Heath I et al. Characterization of 11 novel mutations in the tissue non-specific alkaline phosphatase gene responsible for hypophosphatasia and genotype-phenotype correlations. Mol Genet Metab. 2005 Mar;84(3):273-7. Cui Y et al. A systematic review of genetic skeletal disorders reported in Chinese biomedical journals between 1978 and 2012. Orphanet J Rare Dis. 2012 Aug 22;7:55. Fauvert D et al. Mild forms of hypophosphatasia mostly result from dominant negative effect of severe alleles or from compound heterozygosity for severe and moderate alleles. BMC Med Genet. 2009 Jun 6;10:51. Mumm S et al. Denaturing gradient gel electrophoresis analysis of the tissue nonspecific alkaline phosphatase isoenzyme gene in hypophosphatasia. Mol Genet Metab. 2002 Feb;75(2):143-53. Taillandier A et al. Characterization of eleven novel mutations (M45L, R119H, 544delG, G145V, H154Y, C184Y, D289V, 862+5A, 1172delC, R411X, E459K) in the tissue-nonspecific alkaline phosphatase (TNSALP) gene in patients with severe hypophosphatasia. Mutations in brief no. 217. Online. Hum Mutat. 1999;13(2):171-2. Taillandier A et al. Twelve novel mutations in the tissue-nonspecific alkaline phosphatase gene (ALPL) in patients with various forms of hypophosphatasia. Hum Mutat. 2001;18(1):83-4. Taillandier A et al. Genetic analysis of adults heterozygous for ALPL mutations. J Bone Miner Metab. 2018 Nov;36(6):723-733. Taketani T et al. Clinical and genetic aspects of hypophosphatasia in Japanese patients. Arch Dis Child. 2014 Mar;99(3):211-5. Whyte MP et al. Enzyme-replacement therapy in life-threatening hypophosphatasia. N Engl J Med. 2012 Mar 8;366(10):904-13. Whyte MP et al. Hypophosphatasia: validation and expansion of the clinical nosology for children from 25 years experience with 173 pediatric patients. Bone. 2015 Jun;75:229-39. Yang H et al. Characterization of six missense mutations in the tissue-nonspecific alkaline phosphatase (TNSALP) gene in Chinese children with hypophosphatasia. Cell Physiol Biochem. 2013;32(3):635-44.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 136 of the ALPL protein (p.Arg136His). This variant is present in population databases (rs121918011, gnomAD 0.02%). This missense change has been observed in individuals with hypophosphatasia (PMID: 10094560, 11438998, 11855933, 15694177, 19500388, 25731960, 26783040). This variant is also known as Arg119His. ClinVar contains an entry for this variant (Variation ID: 13675). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ALPL protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ALPL function (PMID: 10332035, 19500388). This variant disrupts the p.Arg136 amino acid residue in ALPL. Other variant(s) that disrupt this residue have been observed in individuals with ALPL-related conditions (PMID: 19500388, 22913777, 24022022), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

Has also been reported as a single heterozygous variant in association with an odonto form and an adult form of hypophosphatasia (PMID: 19500388, 31707452); Published functional studies demonstrate a damaging effect as protein harboring the R136H variant has approximately 33% of the residual activity of wild-type protein (PMID: 19500388, 10332035); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 22913777, 34712267, 34758253, 11438998, 11855933, 11395499, 25023282, 10332035, 28506345, 26783040, 31600233, 31760938, 31707452, 29236161, 15694177, 10094560, 34213743, 34189384, 31589614, 32956941, 33452237, 33549410, 35314707, 35726512, 36444396, 36352425, 32160374, 36708496, 19500388)

The ALPL c.407G>A (p.Arg136His) missense variant has been reported in at least seven studies in which it is found in a compound heterozygous state in eight individuals with hypophosphatasia, including two with the infantile form, two with the childhood form, and four with mild symptoms, and in a heterozygous state in two individuals with the adult form of hypophosphatasia. The p.Arg136His variant was also found in a heterozygous state in two asymptomatic parents with low alkaline phosphatase activity and one asymptomatic individual with unknown alkaline phosphatase activity (Taillandier et al. 1998; Taillandier et al. 2001; Mumm et al. 2002; Brun-Heath et al. 2005; Fauvert et al. 2009; Cui et al. 2012; Riancho-Zarrabeitia et al. 2016). The p.Arg136His variant appears to be associated with more severe clinical symptoms when expressed in a compound heterozygous state with an additional ALPL variant. Control data are unavailable for this variant, which is reported at a frequency of 0.00030 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies demonstrated that the p.Arg136His variant protein displays one-third of the activity of the wild type alkaline phosphatase and does not have a dominant-negative effect when co-expressed with the wild type form (Zurutuza et al. 1999; Fauvert et al. 2009). Based on the collective evidence, the p.Arg136His variant is classified as pathogenic for hypophosphatasia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

ACMG Criteria: PS3, PS4, PM1, PM2, PM3, PM5, PP1, PP3, PP4, PP5; Variant was found in heterozygous state.

Variant summary: ALPL c.407G>A (p.Arg136His) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 250880 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in ALPL causing Hypophosphatasia (0.00014 vs 0.0035), allowing no conclusion about variant significance. c.407G>A has been reported in the literature as compound heterozygous genotype in multiple individuals affected with autosomal recessive Hypophosphatasia and a fetus with skeletal dysplasia (Taillandier_1999, Okawa_2019, Zhang_2021, del Angel_2020, Bai_2022). These data indicate that the variant is very likely to be associated with disease. A different variant affecting the same codon has been classified as pathogenic by our lab (c.406C>T, p.Arg136Cys), supporting the critical relevance of codon 136 to ALPL protein function. Two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% residual enzymatic activity of the wild type protein and this variant has also been shown to have a dominant negative effect (Fauvert_2009, del Angel_2020). The following publications have been ascertained in the context of this evaluation (PMID: 36352425, 19500388, 31707452, 31600233, 10094560, 34712267, 32160374). ClinVar contains an entry for this variant (Variation ID: 13675). Based on the evidence outlined above, the variant was classified as pathogenic.

ALPL: PM1, PM2, PM5, PS4:Moderate, PP4, PS3:Supporting