NM_000478.6(ALPL):c.1403C>T (p.Ala468Val) AND Adult hypophosphatasia

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Oct 13, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002464210.2

Allele description [Variation Report for NM_000478.6(ALPL):c.1403C>T (p.Ala468Val)]

NM_000478.6(ALPL):c.1403C>T (p.Ala468Val)

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.1403C>T (p.Ala468Val)

HGVS:

NC_000001.11:g.21577476C>T
NG_008940.1:g.73112C>T
NM_000478.6:c.1403C>TMANE SELECT
NM_001127501.4:c.1238C>T
NM_001177520.3:c.1172C>T
NM_001369803.2:c.1403C>T
NM_001369804.2:c.1403C>T
NM_001369805.2:c.1403C>T
NP_000469.3:p.Ala468Val
NP_001120973.2:p.Ala413Val
NP_001170991.1:p.Ala391Val
NP_001356732.1:p.Ala468Val
NP_001356733.1:p.Ala468Val
NP_001356734.1:p.Ala468Val
NC_000001.10:g.21903969C>T
NM_000478.5:c.1403C>T

Protein change:

A391V

Links:

dbSNP: rs766656419

NCBI 1000 Genomes Browser:

rs766656419

Molecular consequence:

NM_000478.6:c.1403C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127501.4:c.1238C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001177520.3:c.1172C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369803.2:c.1403C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369804.2:c.1403C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369805.2:c.1403C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Adult hypophosphatasia
Identifiers:: MedGen: C0268413; Orphanet: 436; OMIM: 146300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002759364	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 7, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004191948	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 13, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002759364

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 7, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004191948

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 13, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV002759364.1

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

#	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

From Baylor Genetics, SCV004191948.1

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

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

Last Updated: Feb 28, 2024

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