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NM_000543.5(SMPD1):c.8G>A (p.Arg3His) AND SMPD1-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 17, 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:
RCV003417882.5

Allele description [Variation Report for NM_000543.5(SMPD1):c.8G>A (p.Arg3His)]

NM_000543.5(SMPD1):c.8G>A (p.Arg3His)

Genes:
LOC130005193:ATAC-STARR-seq lymphoblastoid silent region 3099 [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.8G>A (p.Arg3His)
HGVS:
  • NC_000011.10:g.6390606G>A
  • NG_011780.1:g.5182G>A
  • NM_000543.5:c.8G>AMANE SELECT
  • NM_001007593.3:c.8G>A
  • NM_001318087.2:c.8G>A
  • NM_001318088.2:c.-954G>A
  • NM_001365135.2:c.8G>A
  • NP_000534.3:p.Arg3His
  • NP_001007594.2:p.Arg3His
  • NP_001305016.1:p.Arg3His
  • NP_001352064.1:p.Arg3His
  • NC_000011.9:g.6411836G>A
  • NM_000543.4:c.8G>A
  • NR_027400.3:n.133G>A
  • NR_134502.2:n.133G>A
Protein change:
R3H
Links:
dbSNP: rs199836262
NCBI 1000 Genomes Browser:
rs199836262
Molecular consequence:
  • NM_001318088.2:c.-954G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000543.5:c.8G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007593.3:c.8G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318087.2:c.8G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365135.2:c.8G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.133G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.133G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004116522PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 17, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004116522.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The SMPD1 c.8G>A variant is predicted to result in the amino acid substitution p.Arg3His. This variant has been reported in the heterozygous state in an individual with a lysosomal storage disorder, however no additional evidence was provided to support the pathogenicity of this variant (see Table 5 in Fernández-Marmiesse et al. 2014. PubMed ID: 24767253). This variant is reported in 0.11% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-6411836-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Sep 29, 2024