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NM_000543.5(SMPD1):c.362T>C (p.Leu121Pro) AND Niemann-Pick disease, type A

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Apr 25, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV000671945.3

Allele description [Variation Report for NM_000543.5(SMPD1):c.362T>C (p.Leu121Pro)]

NM_000543.5(SMPD1):c.362T>C (p.Leu121Pro)

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.362T>C (p.Leu121Pro)
HGVS:
  • NC_000011.10:g.6391427T>C
  • NG_011780.1:g.6003T>C
  • NM_000543.5:c.362T>CMANE SELECT
  • NM_001007593.3:c.359T>C
  • NM_001318087.2:c.362T>C
  • NM_001318088.2:c.-600T>C
  • NM_001365135.2:c.362T>C
  • NP_000534.3:p.Leu121Pro
  • NP_001007594.2:p.Leu120Pro
  • NP_001305016.1:p.Leu121Pro
  • NP_001352064.1:p.Leu121Pro
  • NC_000011.9:g.6412657T>C
  • NM_000543.4:c.362T>C
  • NR_027400.3:n.487T>C
  • NR_134502.2:n.487T>C
Protein change:
L120P
Links:
dbSNP: rs1554934109
NCBI 1000 Genomes Browser:
rs1554934109
Molecular consequence:
  • NM_001318088.2:c.-600T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000543.5:c.362T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007593.3:c.359T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318087.2:c.362T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365135.2:c.362T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.487T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.487T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000796989Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Uncertain significance
(Jan 8, 2018)
unknownclinical testing

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

Citation Link,

SCV004205509Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Apr 25, 2023)
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

Rapid Diagnosis of 83 Patients with Niemann Pick Type C Disease and Related Cholesterol Transport Disorders by Cholestantriol Screening.

Reunert J, Fobker M, Kannenberg F, Du Chesne I, Plate M, Wellhausen J, Rust S, Marquardt T.

EBioMedicine. 2016 Feb;4:170-5. doi: 10.1016/j.ebiom.2015.12.018.

PubMed [citation]
PMID:
26981555
PMCID:
PMC4776073

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 Counsyl, SCV000796989.1

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

From Baylor Genetics, SCV004205509.1

#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: Feb 4, 2024