NM_000543.5(SMPD1):c.1474G>A (p.Gly492Ser) AND Niemann-Pick disease, type B

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 22, 2021
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:: RCV001579139.3

Allele description [Variation Report for NM_000543.5(SMPD1):c.1474G>A (p.Gly492Ser)]

NM_000543.5(SMPD1):c.1474G>A (p.Gly492Ser)

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.1474G>A (p.Gly492Ser)

HGVS:

NC_000011.10:g.6394029G>A
NG_011780.1:g.8605G>A
NG_029615.1:g.30386C>T
NM_000543.5:c.1474G>AMANE SELECT
NM_001007593.3:c.1471G>A
NM_001318087.2:c.1474G>A
NM_001318088.2:c.553G>A
NM_001365135.2:c.1342G>A
NP_000534.3:p.Gly492Ser
NP_001007594.2:p.Gly491Ser
NP_001305016.1:p.Gly492Ser
NP_001305017.1:p.Gly185Ser
NP_001352064.1:p.Gly448Ser
NC_000011.9:g.6415259G>A
NM_000543.4(SMPD1):c.1474G>A
NM_000543.4:c.1474G>A
NR_027400.3:n.1427G>A
NR_134502.2:n.946G>A
p.Gly492Ser

Protein change:

G185S

Links:

dbSNP: rs144873307

NCBI 1000 Genomes Browser:

rs144873307

Molecular consequence:

NM_000543.5:c.1474G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001007593.3:c.1471G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318087.2:c.1474G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318088.2:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365135.2:c.1342G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_027400.3:n.1427G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.946G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Niemann-Pick disease, type B
Identifiers:: MONDO: MONDO:0011871; MedGen: C0268243; Orphanet: 77293; OMIM: 607616

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001806558	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]
SCV003841203	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV001806558

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]

SCV003841203

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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
not provided	germline	no	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, SCV001806558.1

#	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, SCV003841203.1

#	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: Jan 19, 2025

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