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NM_000543.5(SMPD1):c.1101dup (p.Phe368fs) AND Niemann-Pick disease, type A

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Mar 11, 2024
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:
RCV000668954.2

Allele description [Variation Report for NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)]

NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)

Gene:
SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)
Other names:
p.Phe368ValfsTer23
HGVS:
  • NC_000011.10:g.6393225dup
  • NG_011780.1:g.7801dup
  • NG_029615.1:g.31195dup
  • NM_000543.5:c.1101dupMANE SELECT
  • NM_001007593.3:c.1098dup
  • NM_001318087.2:c.1101dup
  • NM_001318088.2:c.180dup
  • NM_001365135.2:c.1132-392dup
  • NP_000534.3:p.Phe368fs
  • NP_001007594.2:p.Phe367fs
  • NP_001305016.1:p.Phe368fs
  • NP_001305017.1:p.Phe61fs
  • NC_000011.9:g.6414449_6414450insG
  • NC_000011.9:g.6414455dup
  • NM_000543.4:c.1101dupG
  • NR_134502.2:n.573dup
Protein change:
F367fs
Links:
dbSNP: rs1422720020
NCBI 1000 Genomes Browser:
rs1422720020
Molecular consequence:
  • NM_000543.5:c.1101dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001007593.3:c.1098dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318087.2:c.1101dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318088.2:c.180dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001365135.2:c.1132-392dup - intron variant - [Sequence Ontology: SO:0001627]
  • NR_134502.2:n.573dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Functional consequence:
loss_of_function_variant [Sequence Ontology: SO:0002054]

Condition(s)

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000793638Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Likely pathogenic
(Aug 31, 2017)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV005052841Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 11, 2024)
unknownclinical testing

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

Summary from all submissions

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

Citations

PubMed

Identification of a distinct mutation spectrum in the SMPD1 gene of Chinese patients with acid sphingomyelinase-deficient Niemann-Pick disease.

Zhang H, Wang Y, Gong Z, Li X, Qiu W, Han L, Ye J, Gu X.

Orphanet J Rare Dis. 2013 Jan 28;8:15. doi: 10.1186/1750-1172-8-15.

PubMed [citation]
PMID:
23356216
PMCID:
PMC3566977

Spectrum of SMPD1 mutations in Asian-Indian patients with acid sphingomyelinase (ASM)-deficient Niemann-Pick disease.

Ranganath P, Matta D, Bhavani GS, Wangnekar S, Jain JM, Verma IC, Kabra M, Puri RD, Danda S, Gupta N, Girisha KM, Sankar VH, Patil SJ, Ramadevi AR, Bhat M, Gowrishankar K, Mandal K, Aggarwal S, Tamhankar PM, Tilak P, Phadke SR, Dalal A.

Am J Med Genet A. 2016 Oct;170(10):2719-30. doi: 10.1002/ajmg.a.37817. Epub 2016 Jun 24.

PubMed [citation]
PMID:
27338287
See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000793638.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV005052841.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 17, 2024