NM_000478.6(ALPL):c.1250A>G (p.Asn417Ser) AND Hypophosphatasia

Clinical significance:Pathogenic (Last evaluated: Aug 5, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001194283.2

Allele description [Variation Report for NM_000478.6(ALPL):c.1250A>G (p.Asn417Ser)]

NM_000478.6(ALPL):c.1250A>G (p.Asn417Ser)

Gene:
ALPL:alkaline phosphatase, biomineralization associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.12
Genomic location:
Preferred name:
NM_000478.6(ALPL):c.1250A>G (p.Asn417Ser)
Other names:
N400S
HGVS:
  • NC_000001.11:g.21576582A>G
  • NG_008940.1:g.72218A>G
  • NM_000478.6:c.1250A>GMANE SELECT
  • NM_001127501.4:c.1085A>G
  • NM_001177520.3:c.1019A>G
  • NM_001369803.2:c.1250A>G
  • NM_001369804.2:c.1250A>G
  • NM_001369805.2:c.1250A>G
  • NP_000469.3:p.Asn417Ser
  • NP_001120973.2:p.Asn362Ser
  • NP_001170991.1:p.Asn340Ser
  • NP_001356732.1:p.Asn417Ser
  • NP_001356733.1:p.Asn417Ser
  • NP_001356734.1:p.Asn417Ser
  • NC_000001.10:g.21903075A>G
  • NM_000478.4:c.1250A>G
  • NM_000478.5:c.1250A>G
  • P05186:p.Asn417Ser
Protein change:
N340S; ASN400SER
Links:
UniProtKB: P05186#VAR_025937; OMIM: 171760.0017; dbSNP: rs121918014
NCBI 1000 Genomes Browser:
rs121918014
Molecular consequence:
  • NM_000478.6:c.1250A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127501.4:c.1085A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177520.3:c.1019A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369803.2:c.1250A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369804.2:c.1250A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369805.2:c.1250A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypophosphatasia
Synonyms:
Phosphoethanol-aminuria; Hypophosphatasia mild
Identifiers:
MONDO: MONDO:0018570; MedGen: C0020630

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001363683Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Pathogenic
(Aug 5, 2019)
germlineclinical testing

PubMed (9)
[See all records that cite these PMIDs]

Citation Link,

SCV001749798GenomeConnect - Invitae Patient Insights Networkno assertion providednot providedunknownphenotyping only

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedphenotyping only

Citations

PubMed

Mild forms of hypophosphatasia mostly result from dominant negative effect of severe alleles or from compound heterozygosity for severe and moderate alleles.

Fauvert D, Brun-Heath I, Lia-Baldini AS, Bellazi L, Taillandier A, Serre JL, de Mazancourt P, Mornet E.

BMC Med Genet. 2009 Jun 6;10:51. doi: 10.1186/1471-2350-10-51.

PubMed [citation]
PMID:
19500388
PMCID:
PMC2702372

Mutational and biochemical findings in adults with persistent hypophosphatasemia.

McKiernan FE, Dong J, Berg RL, Scotty E, Mundt P, Larson L, Rai I.

Osteoporos Int. 2017 Aug;28(8):2343-2348. doi: 10.1007/s00198-017-4035-y. Epub 2017 Apr 12.

PubMed [citation]
PMID:
28401263
See all PubMed Citations (9)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363683.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

Variant summary: ALPL c.1250A>G (p.Asn417Ser) results in a conservative amino acid change located in the Crown domain (Simon-Bouy_2008) of 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 2e-05 in 251442 control chromosomes (gnomAD). c.1250A>G has been reported in the literature as a single heterozygous variant (i.e. no other variants detected) in multiple individuals with features of mild HPP (odontohypophosphatasia, adult and childhood hypophosphatasia) but also in at least 2 parents that were carriers of the variant without any reported symptoms (Fauvert_2009, Reibel_2009, Whyte_2015). It has also been reported in compound heterozygous state with other pathogenic variants in patients affected with severe perinatal or severe childhood hypophosphatasia (Sergi_2001, Whyte_2015). These data indicate that the variant is very likely to be associated with disease. Using a cell system Fauvert et al reported that this variant has a dominant negative effect (Fauvert_2009) on wild-type enzymatic activity. In addition, Sultana et al performed several functional experiments using an in vitro system and concluded that a complete loss of ALP enzymatic activity resulting from the disruption of its functional dimer structure may represent the molecular basis of HPP associated with ALPL N417S (Sultana_2013). Three ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GenomeConnect - Invitae Patient Insights Network, SCV001749798.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedphenotyping onlynot provided

Description

Variant interpreted as Pathogenic and reported on 11-16-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 17, 2021

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