NM_000543.5(SMPD1):c.152A>T (p.Asp51Val) AND Niemann-Pick disease, type A

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Nov 18, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001579137.5

Allele description [Variation Report for NM_000543.5(SMPD1):c.152A>T (p.Asp51Val)]

NM_000543.5(SMPD1):c.152A>T (p.Asp51Val)

Gene:

SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.152A>T (p.Asp51Val)

HGVS:

NC_000011.10:g.6390750A>T
NG_011780.1:g.5326A>T
NM_000543.5:c.152A>TMANE SELECT
NM_001007593.3:c.152A>T
NM_001318087.2:c.152A>T
NM_001318088.2:c.-810A>T
NM_001365135.2:c.152A>T
NP_000534.3:p.Asp51Val
NP_001007594.2:p.Asp51Val
NP_001305016.1:p.Asp51Val
NP_001352064.1:p.Asp51Val
NC_000011.9:g.6411980A>T
NM_000543.4:c.152A>T
NR_027400.3:n.277A>T
NR_134502.2:n.277A>T

Protein change:

D51V

Links:

dbSNP: rs748589919

NCBI 1000 Genomes Browser:

rs748589919

Molecular consequence:

NM_001318088.2:c.-810A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.152A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001007593.3:c.152A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318087.2:c.152A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365135.2:c.152A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_027400.3:n.277A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.277A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Niemann-Pick disease, type A
Synonyms:: SPHINGOMYELIN LIPIDOSIS; SPHINGOMYELINASE DEFICIENCY
Identifiers:: MONDO: MONDO:0009756; MedGen: C0268242; Orphanet: 77292; OMIM: 257200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001806555	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 22, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004203210	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 18, 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

SCV001806555

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 22, 2021)

germline

clinical testing

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

SCV004203210

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 18, 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	no	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 Genome-Nilou Lab, SCV001806555.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004203210.2

#	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: Jun 17, 2024

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