NM_000543.5(SMPD1):c.83C>T (p.Pro28Leu) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001357849.1

Allele description [Variation Report for NM_000543.5(SMPD1):c.83C>T (p.Pro28Leu)]

NM_000543.5(SMPD1):c.83C>T (p.Pro28Leu)

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.83C>T (p.Pro28Leu)
HGVS:
  • NC_000011.10:g.6390681C>T
  • NG_011780.1:g.5257C>T
  • NM_000543.5:c.83C>TMANE SELECT
  • NM_001007593.3:c.83C>T
  • NM_001318087.2:c.83C>T
  • NM_001318088.2:c.-879C>T
  • NM_001365135.2:c.83C>T
  • NP_000534.3:p.Pro28Leu
  • NP_001007594.2:p.Pro28Leu
  • NP_001305016.1:p.Pro28Leu
  • NP_001352064.1:p.Pro28Leu
  • NC_000011.9:g.6411911C>T
  • NM_000543.4:c.83C>T
  • NR_027400.3:n.208C>T
  • NR_134502.2:n.208C>T
Protein change:
P28L
Links:
dbSNP: rs556155962
NCBI 1000 Genomes Browser:
rs556155962
Molecular consequence:
  • NM_001318088.2:c.-879C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000543.5:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007593.3:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318087.2:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365135.2:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.208C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.208C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001553438Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553438.1

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

Description

The SMPD1 p.Pro28Leu variant was not identified in the literature but was identified in dbSNP (ID: rs556155962) and ClinVar (classified as likely benign by EGL Genetics). The variant was identified in control databases in 143 of 275324 chromosomes (2 homozygous) at a frequency of 0.0005194 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 140 of 30476 chromosomes (freq: 0.004594), Other in 1 of 7038 chromosomes (freq: 0.000142), African in 1 of 23448 chromosomes (freq: 0.000043) and Latino in 1 of 35150 chromosomes (freq: 0.000028), but was not observed in the Ashkenazi Jewish, East Asian, European (Finnish), or European (non-Finnish) populations. The p.Pro28 residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Nov 27, 2021

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