NM_000478.6(ALPL):c.649-1G>A AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 28, 2023
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:: RCV001970877.3

Allele description [Variation Report for NM_000478.6(ALPL):c.649-1G>A]

NM_000478.6(ALPL):c.649-1G>A

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.649-1G>A

HGVS:

NC_000001.11:g.21568103G>A
NG_008940.1:g.63739G>A
NG_008940.2:g.64121G>A
NM_000478.6:c.649-1G>AMANE SELECT
NM_001127501.4:c.484-1G>A
NM_001177520.3:c.418-1G>A
NM_001369803.2:c.649-1G>A
NM_001369804.2:c.649-1G>A
NM_001369805.2:c.649-1G>A
NC_000001.10:g.21894596G>A

Links:

dbSNP: rs2148171286

NCBI 1000 Genomes Browser:

rs2148171286

Molecular consequence:

NM_000478.6:c.649-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001127501.4:c.484-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001177520.3:c.418-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001369803.2:c.649-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001369804.2:c.649-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001369805.2:c.649-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Lactiplantibacillus plantarum strain a80 16S ribosomal RNA gene, partial sequenc...
Lactiplantibacillus plantarum strain a80 16S ribosomal RNA gene, partial sequence
gi|1114444197|gb|KX057561.1|

Nucleotide
txid1590[orgn] AND "strain CCM 1904 ATCC 8014"[All Fields] (10)
Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002265210	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Feb 28, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16199547, 3174660, 10679946, 32973344, 33814268, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002265210

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Feb 28, 2023)

germline

clinical testing

PubMed (6)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

A missense mutation in the human liver/bone/kidney alkaline phosphatase gene causing a lethal form of hypophosphatasia.

Weiss MJ, Cole DE, Ray K, Whyte MP, Lafferty MA, Mulivor RA, Harris H.

Proc Natl Acad Sci U S A. 1988 Oct;85(20):7666-9.

PubMed [citation]

PMID:: 3174660
PMCID:: PMC282253

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV002265210.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change affects an acceptor splice site in intron 6 of the ALPL gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ALPL are known to be pathogenic (PMID: 3174660, 10679946, 32973344, 33814268). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ALPL-related conditions. ClinVar contains an entry for this variant (Variation ID: 1473817). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#	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: Mar 5, 2024

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