NM_000478.6(ALPL):c.319G>A (p.Val107Ile) AND Hypophosphatasia

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 9, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004555139.1

Allele description [Variation Report for NM_000478.6(ALPL):c.319G>A (p.Val107Ile)]

NM_000478.6(ALPL):c.319G>A (p.Val107Ile)

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.319G>A (p.Val107Ile)

HGVS:

NC_000001.11:g.21563131G>A
NG_008940.1:g.58767G>A
NG_008940.2:g.59149G>A
NM_000478.6:c.319G>AMANE SELECT
NM_001127501.4:c.154G>A
NM_001177520.3:c.88G>A
NM_001369803.2:c.319G>A
NM_001369804.2:c.319G>A
NM_001369805.2:c.319G>A
NP_000469.3:p.Val107Ile
NP_001120973.2:p.Val52Ile
NP_001170991.1:p.Val30Ile
NP_001356732.1:p.Val107Ile
NP_001356733.1:p.Val107Ile
NP_001356734.1:p.Val107Ile
NC_000001.10:g.21889624G>A

Protein change:

V107I

Molecular consequence:

NM_000478.6:c.319G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127501.4:c.154G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001177520.3:c.88G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369803.2:c.319G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369804.2:c.319G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369805.2:c.319G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005043787	JKU Lab, Dept of Paediatrics, Johannes Kepler University	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 9, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 38130758, 30049651, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005043787

JKU Lab, Dept of Paediatrics, Johannes Kepler University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 9, 2024)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The Effect of Asfotase Alfa on Plasma and Urine Pyrophosphate Levels and Pseudofractures in a Patient With Adult-Onset Hypophosphatasia.

Hidaka N, Murata H, Tachikawa K, Osaki K, Sekiyama T, Kinoshita Y, Kato H, Hoshino Y, Kimura S, Sunouchi T, Watanabe S, Nangaku M, Makita N, Michigami T, Ito N.

JBMR Plus. 2023 Dec;7(12):e10842. doi: 10.1002/jbm4.10842.

PubMed [citation]

PMID:: 38130758
PMCID:: PMC10731098

Pyridoxal 5'-phosphate and related metabolites in hypophosphatasia: Effects of enzyme replacement therapy.

Akiyama T, Kubota T, Ozono K, Michigami T, Kobayashi D, Takeyari S, Sugiyama Y, Noda M, Harada D, Namba N, Suzuki A, Utoyama M, Kitanaka S, Uematsu M, Mitani Y, Matsunami K, Takishima S, Ogawa E, Kobayashi K.

Mol Genet Metab. 2018 Sep;125(1-2):174-180. doi: 10.1016/j.ymgme.2018.07.006. Epub 2018 Jul 17.

PubMed [citation]

PMID:: 30049651

See all PubMed Citations (3)

Details of each submission

From JKU Lab, Dept of Paediatrics, Johannes Kepler University, SCV005043787.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The variant is absent from GnomAD. The ACMG criteria applied can be looked up in the ALPL gene variant database. https://alplmutationdatabase.jku.at/

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 26, 2024

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