NM_000543.5(SMPD1):c.739G>A (p.Gly247Ser) AND Niemann-Pick disease, type A

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Mar 26, 2024
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:: RCV000169278.4

Allele description [Variation Report for NM_000543.5(SMPD1):c.739G>A (p.Gly247Ser)]

NM_000543.5(SMPD1):c.739G>A (p.Gly247Ser)

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.739G>A (p.Gly247Ser)

HGVS:

NC_000011.10:g.6391804G>A
NG_011780.1:g.6380G>A
NM_000543.5:c.739G>AMANE SELECT
NM_001007593.3:c.736G>A
NM_001318087.2:c.739G>A
NM_001318088.2:c.-223G>A
NM_001365135.2:c.739G>A
NP_000534.3:p.Gly247Ser
NP_001007594.2:p.Gly246Ser
NP_001305016.1:p.Gly247Ser
NP_001352064.1:p.Gly247Ser
NC_000011.9:g.6413034G>A
NM_000543.4(SMPD1):c.739G>A
NM_000543.4:c.739G>A
NR_027400.3:n.864G>A
p.Arg240Gln
p.Gly247Ser

Protein change:

G246S

Links:

dbSNP: rs587779408

NCBI 1000 Genomes Browser:

rs587779408

Molecular consequence:

NM_001318088.2:c.-223G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001007593.3:c.736G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318087.2:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365135.2:c.739G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_027400.3:n.864G>A - 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
SCV000220585	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Likely pathogenic (Aug 10, 2014)	unknown	literature only	PubMed (8) [See all records that cite these PMIDs] 24767253, 12369017, 15241805, 19405096, 23252888, 15234149, 23430884, 15221801 Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015), Citation Link,
SCV001527397	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 26, 2024)	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

SCV000220585

Counsyl

criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))

Likely pathogenic
(Aug 10, 2014)

unknown

literature only

PubMed (8)
[See all records that cite these PMIDs]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV001527397

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 26, 2024)

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, literature only

Citations

PubMed

Assessment of a targeted resequencing assay as a support tool in the diagnosis of lysosomal storage disorders.

Fernández-Marmiesse A, Morey M, Pineda M, Eiris J, Couce ML, Castro-Gago M, Fraga JM, Lacerda L, Gouveia S, Pérez-Poyato MS, Armstrong J, Castiñeiras D, Cocho JA.

Orphanet J Rare Dis. 2014 Apr 25;9:59. doi: 10.1186/1750-1172-9-59.

PubMed [citation]

PMID:: 24767253
PMCID:: PMC4024120

The demographics and distribution of type B Niemann-Pick disease: novel mutations lead to new genotype/phenotype correlations.

Simonaro CM, Desnick RJ, McGovern MM, Wasserstein MP, Schuchman EH.

Am J Hum Genet. 2002 Dec;71(6):1413-9. Epub 2002 Oct 4.

PubMed [citation]

PMID:: 12369017
PMCID:: PMC378582

See all PubMed Citations (9)

Details of each submission

From Counsyl, SCV000220585.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (8)

#	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

From Baylor Genetics, SCV001527397.2

#	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: Sep 29, 2024

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