The ALPL gene variant project: results of the first 100 reclassified variants Article Swipe
Mariam R. Farman
,
Theodora Malli
,
Catherine Rehder
,
Gerald Webersinke
,
Cheryl R. Greenberg
,
Kathryn Dahir
,
Gabriel Ángel Martos‐Moreno
,
Agnès Linglart
,
Keiichi Ozono
,
Lothar Seefried
,
Guillermo del Angel
,
Francesca Barbazza
,
Shapour Reza Shojaei
,
Jessica Ebner
,
Florian Högler
,
Erica Nading
,
Erin Huggins
,
Eric T. Rush
,
Ahmed El‐Gazzar
,
Josephine T. Tauer
,
Priya S. Kishnani
,
Wolfgang Högler
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/jbmrpl/ziaf044
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/jbmrpl/ziaf044
Hypophosphatasia (HPP) is an inherited disorder that affects bone and tooth mineralization, among other body systems. HPP is caused by pathogenic variants in the alkaline phosphatase-liver (ALPL) gene, which encodes tissue nonspecific alkaline phosphatase. One major challenge in diagnosing HPP is interpreting variant of uncertain significance (VUS), which can create uncertainty for patients and healthcare professionals, leading to delays in diagnosis and treatment or incorrect diagnoses. Since February 2021, the ALPLgene variant consortium has reclassified 100 VUS using adjusted American College of Medical Genetics/Association for Molecular Pathology criteria. Of these, 11 were reclassified as pathogenic, 62 as likely pathogenic, three as likely benign, one as benign, and 23 remained as VUS; out of 100 variants, there were 81 missense, eight frameshifts, four in-frame deletions, two intronic, two synonymous, two nonsense, and one splice site variant. In vitrofunctional testing of the variant’s residual enzymatic activity and its dominant negative effect (DNE) was required for 40 variants.Out of 40 variants tested, 72% showed <30% residual activity and were reclassified as pathogenic or likely pathogenic. Among these, 48% exhibited a DNE. All variants with ˂15% residual activity showed a DNE, while those with over 20% did not. In terms of domains, all tested variants in the active site domain and 75% of those in the homodimeric interface showed <30% residual activity. The consortium’s reclassification of 100 ALPLvariants has resulted in a 21% increase in the number of variants in the Johannes Kepler University ALPLgene variant database. Furthermore, 136 new genotypes with 118 associated phenotypes, including asymptomatic states, have been added. These expanded resources will help improve genetic counseling for patients and families affected by ALPLvariants and enable faster diagnosis and medical decision-making.
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- Type
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- Language
- en
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- https://doi.org/10.1093/jbmrpl/ziaf044
- https://academic.oup.com/jbmrplus/advance-article-pdf/doi/10.1093/jbmrpl/ziaf044/62427280/ziaf044.pdf
- OA Status
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- Cited By
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- Related Works
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All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4408534447Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/jbmrpl/ziaf044Digital Object Identifier
- Title
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The ALPL gene variant project: results of the first 100 reclassified variantsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-03-17Full publication date if available
- Authors
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Mariam R. Farman, Theodora Malli, Catherine Rehder, Gerald Webersinke, Cheryl R. Greenberg, Kathryn Dahir, Gabriel Ángel Martos‐Moreno, Agnès Linglart, Keiichi Ozono, Lothar Seefried, Guillermo del Angel, Francesca Barbazza, Shapour Reza Shojaei, Jessica Ebner, Florian Högler, Erica Nading, Erin Huggins, Eric T. Rush, Ahmed El‐Gazzar, Josephine T. Tauer, Priya S. Kishnani, Wolfgang HöglerList of authors in order
- Landing page
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https://doi.org/10.1093/jbmrpl/ziaf044Publisher landing page
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https://academic.oup.com/jbmrplus/advance-article-pdf/doi/10.1093/jbmrpl/ziaf044/62427280/ziaf044.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://academic.oup.com/jbmrplus/advance-article-pdf/doi/10.1093/jbmrpl/ziaf044/62427280/ziaf044.pdfDirect OA link when available
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6Total citation count in OpenAlex
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2025: 6Per-year citation counts (last 5 years)
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| publication_date | 2025-03-17 |
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| referenced_works_count | 38 |
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| abstract_inverted_index.11 | 91 |
| abstract_inverted_index.23 | 108 |
| abstract_inverted_index.40 | 154, 157 |
| abstract_inverted_index.62 | 96 |
| abstract_inverted_index.81 | 118 |
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| abstract_inverted_index.Of | 89 |
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| abstract_inverted_index.118 | 249 |
| abstract_inverted_index.136 | 245 |
| abstract_inverted_index.20% | 192 |
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| abstract_inverted_index.48% | 175 |
| abstract_inverted_index.72% | 160 |
| abstract_inverted_index.75% | 208 |
| abstract_inverted_index.All | 179 |
| abstract_inverted_index.HPP | 17, 40 |
| abstract_inverted_index.One | 35 |
| abstract_inverted_index.The | 219 |
| abstract_inverted_index.VUS | 77 |
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| abstract_inverted_index.DNE. | 178 |
| abstract_inverted_index.VUS; | 111 |
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| abstract_inverted_index.(HPP) | 2 |
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| abstract_inverted_index.These | 258 |
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| abstract_inverted_index.which | 29, 48 |
| abstract_inverted_index.while | 188 |
| abstract_inverted_index.˂15% | 182 |
| abstract_inverted_index.(ALPL) | 27 |
| abstract_inverted_index.(VUS), | 47 |
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| abstract_inverted_index.splice | 133 |
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| abstract_inverted_index.these, | 90, 174 |
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| abstract_inverted_index.College | 81 |
| abstract_inverted_index.Medical | 83 |
| abstract_inverted_index.affects | 8 |
| abstract_inverted_index.benign, | 103, 106 |
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| abstract_inverted_index.genetic | 264 |
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| abstract_inverted_index.leading | 57 |
| abstract_inverted_index.medical | 278 |
| abstract_inverted_index.states, | 254 |
| abstract_inverted_index.tested, | 159 |
| abstract_inverted_index.testing | 138 |
| abstract_inverted_index.variant | 43, 72, 242 |
| abstract_inverted_index.ALPLgene | 71, 241 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.American | 80 |
| abstract_inverted_index.February | 68 |
| abstract_inverted_index.Johannes | 238 |
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| abstract_inverted_index.affected | 270 |
| abstract_inverted_index.alkaline | 25, 33 |
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| abstract_inverted_index.domains, | 198 |
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| abstract_inverted_index.families | 269 |
| abstract_inverted_index.in-frame | 123 |
| abstract_inverted_index.increase | 230 |
| abstract_inverted_index.negative | 148 |
| abstract_inverted_index.patients | 53, 267 |
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| abstract_inverted_index.residual | 142, 163, 183, 217 |
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| abstract_inverted_index.systems. | 16 |
| abstract_inverted_index.variant. | 135 |
| abstract_inverted_index.variants | 22, 158, 180, 201, 235 |
| abstract_inverted_index.Molecular | 86 |
| abstract_inverted_index.Pathology | 87 |
| abstract_inverted_index.activity. | 218 |
| abstract_inverted_index.challenge | 37 |
| abstract_inverted_index.criteria. | 88 |
| abstract_inverted_index.database. | 243 |
| abstract_inverted_index.diagnosis | 61, 276 |
| abstract_inverted_index.enzymatic | 143 |
| abstract_inverted_index.exhibited | 176 |
| abstract_inverted_index.genotypes | 247 |
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| abstract_inverted_index.incorrect | 65 |
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| abstract_inverted_index.intronic, | 126 |
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| abstract_inverted_index.counseling | 265 |
| abstract_inverted_index.deletions, | 124 |
| abstract_inverted_index.diagnoses. | 66 |
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| abstract_inverted_index.healthcare | 55 |
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| abstract_inverted_index.nonspecific | 32 |
| abstract_inverted_index.pathogenic, | 95, 99 |
| abstract_inverted_index.pathogenic. | 172 |
| abstract_inverted_index.phenotypes, | 251 |
| abstract_inverted_index.synonymous, | 128 |
| abstract_inverted_index.uncertainty | 51 |
| abstract_inverted_index.variant’s | 141 |
| abstract_inverted_index.ALPLvariants | 224, 272 |
| abstract_inverted_index.Furthermore, | 244 |
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| abstract_inverted_index.reclassified | 75, 93, 167 |
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| abstract_inverted_index.Hypophosphatasia | 1 |
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| abstract_inverted_index.reclassification | 221 |
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