NM_000478.6(ALPL):c.876A>G (p.Pro292=) AND Hypophosphatasia

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 13, 2018
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:: RCV000274166.14

Allele description [Variation Report for NM_000478.6(ALPL):c.876A>G (p.Pro292=)]

NM_000478.6(ALPL):c.876A>G (p.Pro292=)

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.876A>G (p.Pro292=)

HGVS:

NC_000001.11:g.21573678A>G
NG_008940.1:g.69314A>G
NM_000478.6:c.876A>GMANE SELECT
NM_001127501.4:c.711A>G
NM_001177520.3:c.645A>G
NM_001369803.2:c.876A>G
NM_001369804.2:c.876A>G
NM_001369805.2:c.876A>G
NP_000469.3:p.Pro292=
NP_001120973.2:p.Pro237=
NP_001170991.1:p.Pro215=
NP_001356732.1:p.Pro292=
NP_001356733.1:p.Pro292=
NP_001356734.1:p.Pro292=
NC_000001.10:g.21900171A>G
NM_000478.4:c.876A>G
NM_000478.5:c.876A>G
p.Pro292Pro

Links:

dbSNP: rs3200255

NCBI 1000 Genomes Browser:

rs3200255

Molecular consequence:

NM_000478.6:c.876A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127501.4:c.711A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001177520.3:c.645A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369803.2:c.876A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369804.2:c.876A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001369805.2:c.876A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

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DERA [Nestor notabilis]
DERA [Nestor notabilis]
Gene ID:104403703

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000354306	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV001459881	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000354306

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV001459881

Natera, Inc.

no assertion criteria provided

Benign
(Sep 16, 2020)

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000354306.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

From Natera, Inc., SCV001459881.1

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

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

Last Updated: Nov 3, 2024

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