ALPL
alkaline phosphatase, biomineralization associated, the group of Alkaline phosphatases
Basic information
Region (hg38): 1:21509396-21578410
Previous symbols: [ "HOPS" ]
Links
Phenotypes
GenCC
Source:
- hypophosphatasia (Definitive), mode of inheritance: AR
- infantile hypophosphatasia (Definitive), mode of inheritance: AR
- adult hypophosphatasia (Strong), mode of inheritance: AD
- infantile hypophosphatasia (Strong), mode of inheritance: AR
- childhood hypophosphatasia (Definitive), mode of inheritance: AR
- perinatal lethal hypophosphatasia (Supportive), mode of inheritance: AR
- infantile hypophosphatasia (Supportive), mode of inheritance: AR
- childhood hypophosphatasia (Supportive), mode of inheritance: AD
- adult hypophosphatasia (Supportive), mode of inheritance: AD
- odontohypophosphatasia (Supportive), mode of inheritance: AD
- adult hypophosphatasia (Strong), mode of inheritance: AD
- infantile hypophosphatasia (Strong), mode of inheritance: AR
- adult hypophosphatasia (Definitive), mode of inheritance: AD
- childhood hypophosphatasia (Definitive), mode of inheritance: AR
- childhood hypophosphatasia (Definitive), mode of inheritance: AD
- infantile hypophosphatasia (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Hypophosphatasia, infantile; Hypophosphatasia, childhood; Hypophosphatasia, adult; Odontohypophosphatasia | AD/AR | Endocrine; Neurologic | In some forms, abnormal calcium levels can be treated; Seizures can be treated with vitamin B6; Bisphosphonates and excess vitamin D should be avoided due to potential hypercalcemia leading to renal damage; Enzymatic therapy has shown benefit in individuals with severe forms of hypophosphatasia | Dental; Endocrine; Musculoskeletal; Neurologic | 18110134 ; 13800162; 4288761; 4309618 ; 5013867; 7235780; 7305584; 7072744; 7182980; 3960066; 1409720; 3174660; 8406453; 10332035; 10872988; 11479741; 11999978; 12357339; 17519318; 17213282; 21488855; 20978533; 20301329; 22397652 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (832 variants)
- Hypophosphatasia (257 variants)
- Adult hypophosphatasia (171 variants)
- Infantile hypophosphatasia (136 variants)
- Adult hypophosphatasia;Childhood hypophosphatasia;Infantile hypophosphatasia (67 variants)
- not specified (54 variants)
- Childhood hypophosphatasia (41 variants)
- Osteogenesis imperfecta (28 variants)
- Inborn genetic diseases (20 variants)
- ALPL-related condition (15 variants)
- Low alkaline phosphatase (11 variants)
- Adult hypophosphatasia;Infantile hypophosphatasia;Childhood hypophosphatasia (10 variants)
- Infantile hypophosphatasia;Childhood hypophosphatasia;Adult hypophosphatasia (9 variants)
- Childhood hypophosphatasia;Infantile hypophosphatasia;Adult hypophosphatasia (4 variants)
- Childhood hypophosphatasia;Adult hypophosphatasia;Infantile hypophosphatasia (3 variants)
- Odontohypophosphatasia (3 variants)
- Skeletal dysplasia (2 variants)
- Perinatal lethal hypophosphatasia (2 variants)
- Micromelia (2 variants)
- Infantile hypophosphatasia;Adult hypophosphatasia;Childhood hypophosphatasia (1 variants)
- ALPL-related disorders (1 variants)
- Microcephaly (1 variants)
- Osteoporosis (1 variants)
- Hypophosphatemia (1 variants)
- Delayed skeletal maturation (1 variants)
- Connective tissue disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALPL gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 209 | 211 | ||||
| missense | 31 | 146 | 141 | 324 | ||
| nonsense | 13 | 19 | 33 | |||
| start loss | 2 | |||||
| frameshift | 25 | 42 | 67 | |||
| inframe indel | 12 | |||||
| splice donor/acceptor (+/-2bp) | 11 | 19 | ||||
| splice region ? | 2 | 10 | 35 | 1 | 48 | |
| non coding ? | 15 | 102 | 66 | 184 | ||
| Total | 80 | 222 | 164 | 316 | 70 |
Highest pathogenic variant AF is 0.0000658
Variants in ALPL
This is a list of pathogenic ClinVar variants found in the ALPL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-21509428-G-A | Hypophosphatasia • Adult hypophosphatasia;Childhood hypophosphatasia;Infantile hypophosphatasia | Uncertain significance (Jul 09, 2021) | ||
| 1-21509446-C-T | Low alkaline phosphatase • Adult hypophosphatasia;Childhood hypophosphatasia;Infantile hypophosphatasia | Uncertain significance (May 27, 2022) | ||
| 1-21553973-T-C | Childhood hypophosphatasia;Adult hypophosphatasia;Infantile hypophosphatasia | Likely benign (Sep 28, 2021) | ||
| 1-21554001-G-A | Hypophosphatasia | Uncertain significance (Jan 13, 2018) | ||
| 1-21554031-C-T | Hypophosphatasia | Uncertain significance (Jan 13, 2018) | ||
| 1-21554076-T-C | Uncertain significance (Jul 28, 2023) | |||
| 1-21554079-A-C | Uncertain significance (Apr 18, 2023) | |||
| 1-21554082-A-G | Pathogenic (Jan 15, 2021) | |||
| 1-21554084-G-C | Pathogenic (Dec 01, 2023) | |||
| 1-21554090-A-T | Likely benign (May 29, 2023) | |||
| 1-21554098-TA-T | Infantile hypophosphatasia • Hypophosphatasia • Adult hypophosphatasia | Pathogenic (Aug 05, 2023) | ||
| 1-21554102-ACTGGCCATTGG-GTGT | Pathogenic (Oct 14, 2023) | |||
| 1-21554103-C-G | Uncertain significance (Mar 17, 2022) | |||
| 1-21554103-C-T | Likely benign (Oct 15, 2023) | |||
| 1-21554105-G-A | Likely benign (Nov 17, 2023) | |||
| 1-21554106-G-T | Inborn genetic diseases | Uncertain significance (Jun 29, 2023) | ||
| 1-21554107-C-T | Hypophosphatasia • Adult hypophosphatasia;Childhood hypophosphatasia;Infantile hypophosphatasia • Inborn genetic diseases | Uncertain significance (Aug 31, 2022) | ||
| 1-21554110-T-C | Hypophosphatasia | Likely pathogenic (Jun 06, 2023) | ||
| 1-21554113-G-A | Uncertain significance (Aug 02, 2023) | |||
| 1-21554116-C-T | Uncertain significance (Feb 06, 2023) | |||
| 1-21554121-C-T | Hypophosphatasia | Uncertain significance (Oct 20, 2023) | ||
| 1-21554122-T-C | Hypophosphatasia | Likely pathogenic (Dec 16, 2021) | ||
| 1-21554123-TACTA-T | Infantile hypophosphatasia • Skeletal dysplasia • Hypophosphatasia | Pathogenic/Likely pathogenic (Jun 05, 2023) | ||
| 1-21554125-C-G | Hypophosphatasia • ALPL-related disorder | Likely benign (Jan 29, 2024) | ||
| 1-21554126-T-C | Likely benign (Dec 04, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ALPL | protein_coding | protein_coding | ENST00000374840 | 11 | 69048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000364 | 0.998 | 125701 | 0 | 47 | 125748 | 0.000187 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.27 | 266 | 331 | 0.804 | 0.0000210 | 3421 |
| Missense in Polyphen | 110 | 161.7 | 0.68028 | 1678 | ||
| Synonymous | -0.717 | 161 | 150 | 1.07 | 0.0000117 | 1053 |
| Loss of Function | 2.71 | 10 | 24.5 | 0.409 | 0.00000133 | 267 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000478 | 0.000478 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000247 | 0.000246 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: This isozyme may play a role in skeletal mineralization.;
- Disease
- DISEASE: Hypophosphatasia (HOPS) [MIM:146300]: A metabolic bone disease characterized by defective skeletal mineralization and biochemically by deficient activity of the tissue non-specific isoenzyme of alkaline phosphatase. Four forms are distinguished, depending on the age of onset: perinatal, infantile, childhood and adult type. The perinatal form is the most severe and is almost always fatal. The adult form is mild and characterized by recurrent fractures, osteomalacia, rickets, and loss of teeth. Some cases are asymptomatic, while some patients manifest dental features without skeletal manifestations (odontohypophosphatasia). {ECO:0000269|PubMed:10094560, ECO:0000269|PubMed:10332035, ECO:0000269|PubMed:10679946, ECO:0000269|PubMed:10690885, ECO:0000269|PubMed:10834525, ECO:0000269|PubMed:11438998, ECO:0000269|PubMed:11479741, ECO:0000269|PubMed:11745997, ECO:0000269|PubMed:11760847, ECO:0000269|PubMed:11834095, ECO:0000269|PubMed:11855933, ECO:0000269|PubMed:11999978, ECO:0000269|PubMed:12815606, ECO:0000269|PubMed:12920074, ECO:0000269|PubMed:1409720, ECO:0000269|PubMed:15135428, ECO:0000269|PubMed:15694177, ECO:0000269|PubMed:19500388, ECO:0000269|PubMed:22266140, ECO:0000269|PubMed:23039266, ECO:0000269|PubMed:23688511, ECO:0000269|PubMed:25982064, ECO:0000269|PubMed:3174660, ECO:0000269|PubMed:7833929, ECO:0000269|PubMed:8406453, ECO:0000269|PubMed:8954059, ECO:0000269|PubMed:9452105, ECO:0000269|PubMed:9747027, ECO:0000269|PubMed:9781036}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypophosphatasia childhood type (HOPSC) [MIM:241510]: A bone disease characterized by defective skeletal mineralization and biochemically by deficient activity of the tissue non-specific isoenzyme of alkaline phosphatase. {ECO:0000269|PubMed:11760847}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypophosphatasia infantile type (HOPSI) [MIM:241500]: A severe bone disease characterized by defective skeletal mineralization and biochemically by deficient activity of the tissue non-specific isoenzyme of alkaline phosphatase. Three more or less distinct types of infantile hypophosphatasia can be identified: (1) type 1 with onset in utero or in early postnatal life, craniostenosis, severe skeletal abnormalities, hypercalcemia, and death in the first year or so of life; (2) type 2 with later, more gradual development of symptoms, moderately severe 'rachitic' skeletal changes and premature loss of teeth; (3) type 3 with no symptoms, the condition being determined on routine studies. {ECO:0000269|PubMed:10834525, ECO:0000269|PubMed:11438998, ECO:0000269|PubMed:7833929, ECO:0000269|PubMed:8954059}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Folate biosynthesis - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);Hypophosphatasia;Vitamin B6 Metabolism;AGE-RAGE pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;NOTCH1 regulation of human endothelial cell calcification;Role of Osx and miRNAs in tooth development;Endochondral Ossification;regulators of bone mineralization;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.928
Intolerance Scores
- loftool
- 0.0447
- rvis_EVS
- 0.0000761
- rvis_percentile_EVS
- 53.98
Haploinsufficiency Scores
- pHI
- 0.456
- hipred
- Y
- hipred_score
- 0.623
- ghis
- 0.480
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.944
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Alpl
- Phenotype
- muscle phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; reproductive system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- skeletal system development;osteoblast differentiation;endochondral ossification;developmental process involved in reproduction;dephosphorylation;response to lipopolysaccharide;response to vitamin D;response to antibiotic;response to glucocorticoid;cellular response to organic cyclic compound;cementum mineralization
- Cellular component
- extracellular region;plasma membrane;membrane;extracellular matrix;anchored component of membrane;extracellular membrane-bounded organelle;extracellular exosome
- Molecular function
- alkaline phosphatase activity;protein binding;pyrophosphatase activity;metal ion binding