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NM_000543.5(SMPD1):c.1492C>T (p.Arg498Cys) AND SMPD1-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 23, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003955080.2

Allele description [Variation Report for NM_000543.5(SMPD1):c.1492C>T (p.Arg498Cys)]

NM_000543.5(SMPD1):c.1492C>T (p.Arg498Cys)

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.1492C>T (p.Arg498Cys)
HGVS:
  • NC_000011.10:g.6394203C>T
  • NG_011780.1:g.8779C>T
  • NG_029615.1:g.30212G>A
  • NM_000543.4(SMPD1):c.1492C>T
  • NM_000543.5:c.1492C>TMANE SELECT
  • NM_001007593.3:c.1489C>T
  • NM_001318087.2:c.1512C>T
  • NM_001318088.2:c.571C>T
  • NM_001365135.2:c.1360C>T
  • NP_000534.3:p.Arg498Cys
  • NP_001007594.2:p.Arg497Cys
  • NP_001305016.1:p.Thr504=
  • NP_001305017.1:p.Arg191Cys
  • NP_001352064.1:p.Arg454Cys
  • NC_000011.9:g.6415433C>T
  • NM_000543.4(SMPD1):c.1492C>T
  • NM_000543.4:c.1492C>T
  • NM_000543.5:c.1492C>T
  • NR_027400.3:n.1445C>T
  • NR_134502.2:n.984C>T
  • p.Arg498Cys
Protein change:
R191C
Links:
dbSNP: rs769904764
NCBI 1000 Genomes Browser:
rs769904764
Molecular consequence:
  • NM_000543.5:c.1492C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007593.3:c.1489C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318088.2:c.571C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365135.2:c.1360C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.1445C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.984C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001318087.2:c.1512C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
SMPD1-related disorder
Synonyms:
SMPD1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004769358PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(Sep 23, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004769358.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The SMPD1 c.1492C>T variant is predicted to result in the amino acid substitution p.Arg498Cys. This variant has been reported in individuals with Niemann-Pick disease (reported as R496L in Simonaro et al. 2002. PubMed ID: 12369017; Zhang et al. 2013. PubMed ID: 23356216; Hu et al. 2021. PubMed ID: 33675270). This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024