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NM_000543.5(SMPD1):c.28C>T (p.Gln10Ter) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 4, 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:
RCV001386465.4

Allele description [Variation Report for NM_000543.5(SMPD1):c.28C>T (p.Gln10Ter)]

NM_000543.5(SMPD1):c.28C>T (p.Gln10Ter)

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.28C>T (p.Gln10Ter)
HGVS:
  • NC_000011.10:g.6390626C>T
  • NG_011780.1:g.5202C>T
  • NM_000543.5:c.28C>TMANE SELECT
  • NM_001007593.3:c.28C>T
  • NM_001318087.2:c.28C>T
  • NM_001318088.2:c.-934C>T
  • NM_001365135.2:c.28C>T
  • NP_000534.3:p.Gln10Ter
  • NP_001007594.2:p.Gln10Ter
  • NP_001305016.1:p.Gln10Ter
  • NP_001352064.1:p.Gln10Ter
  • NC_000011.9:g.6411856C>T
  • NM_000543.4:c.28C>T
  • NR_027400.3:n.153C>T
  • NR_134502.2:n.153C>T
Protein change:
Q10*
Links:
dbSNP: rs1205990349
NCBI 1000 Genomes Browser:
rs1205990349
Molecular consequence:
  • NM_001318088.2:c.-934C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_027400.3:n.153C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.153C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000543.5:c.28C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001007593.3:c.28C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001318087.2:c.28C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001365135.2:c.28C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001586695Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 4, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

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

Screening of 25 Italian patients with Niemann-Pick A reveals fourteen new mutations, one common and thirteen private, in SMPD1.

Ricci V, Stroppiano M, Corsolini F, Di Rocco M, Parenti G, Regis S, Grossi S, Biancheri R, Mazzotti R, Filocamo M.

Hum Mutat. 2004 Jul;24(1):105.

PubMed [citation]
PMID:
15221801
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001586695.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 550117). This variant has not been reported in the literature in individuals affected with SMPD1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln10*) in the SMPD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SMPD1 are known to be pathogenic (PMID: 12369017, 15221801).

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

Last Updated: Mar 16, 2024