BabyScreen+ newborn screening
Gene: ALPL Green List (high evidence)Green List (high evidence)
Well established gene-disease association.
Clinical signs of the infantile form appear during the first 6 months of life and has high mortality, with 50% succumbing to respiratory failure due to undermineralization of the ribs. The childhood form in most cases presents after the first 6 months of life and before 5 years.
Adult HP presents during middle age, though the patient may have had mild rickets in childhood. Prognosis depends on clinical course and severity. Patients with adult or odonto-HP are believed to have a normal lifespan. AD/AR inheritance reported for these milder forms.
Treatment:
TNSALP ERT has received FDA approval in three settings: perinatal, infantile, and juvenile onset HP. However, the long-term effects of treatment are not fully known. In two prospective, single-arm studies, 68 individuals with severe, perinatal/infantile HP completed 24-weeks of ERT beginning at age 1 day – 78 months. Of patients requiring respiratory support (n = 26), 81% (n = 21) survived through the last date of assessment (median age 3.2 years) versus a 5% survival rate in historical controls. Further, 54 required mechanical ventilation and of these, 91% survived and 85% were ventilator free at last contact, in comparison to 27% overall survival and 25% ventilator free in 48 historical controls. Radiographs from 64 of these individuals indicated improvement on the Radiographic Global Impression of Change (RGI-C) scale (defined as “responders”) in 74% at last assessment, though comparative historical data does not exist. Eighteen individuals with perinatal/infantile HP experienced fractures during treatment; the effect of ERT on fractures remains unclear. In a prospective open-label, single arm study, 8 patients with juvenile HP completed at least 48 months of therapy and were compared to 32 historical controls. By the RGI-C rating of radiographs, all eight patients were deemed responders; two (6%) of the historical controls were rated responders. Gait also improved in patients treated with ERT, with a 6-minute walk test improving to the normal range in six of six patients assessed by month 48, from none at baseline. The data are at present are insufficient to assess the effect of ERT on fractures in juvenile HP. The long-term effects of treatment are not fully known.
Treatment with bisphosphonates, commonly used for rickets, may be detrimental.Created: 21 Sep 2022, 1:28 a.m. | Last Modified: 21 Sep 2022, 1:28 a.m.
Panel Version: 0.81
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Hypophosphatasia, childhood OMIM#241510; Hypophosphatasia, infantile OMIM#241500
Publications
Tag skeletal tag was added to gene: ALPL.
Gene: alpl has been classified as Green List (High Evidence).
Phenotypes for gene: ALPL were changed from Hypophosphatasia, MIM#241500 to Hypophosphatasia, childhood OMIM#241510; Hypophosphatasia, infantile OMIM#241500
Publications for gene: ALPL were set to
Tag treatable tag was added to gene: ALPL.
gene: ALPL was added gene: ALPL was added to gNBS. Sources: BeginNGS,BabySeq Category A gene,Expert Review Green Mode of inheritance for gene: ALPL was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ALPL were set to Hypophosphatasia, MIM#241500
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at panelapp@genomicsengland.co.uk
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.