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NM_000543.5(SMPD1):c.1429C>A (p.Pro477Thr) AND Niemann-Pick disease, type A

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 25, 2021
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:
RCV001527429.2

Allele description [Variation Report for NM_000543.5(SMPD1):c.1429C>A (p.Pro477Thr)]

NM_000543.5(SMPD1):c.1429C>A (p.Pro477Thr)

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.1429C>A (p.Pro477Thr)
HGVS:
  • NC_000011.10:g.6393984C>A
  • NG_011780.1:g.8560C>A
  • NG_029615.1:g.30431G>T
  • NM_000543.5:c.1429C>AMANE SELECT
  • NM_001007593.3:c.1426C>A
  • NM_001318087.2:c.1429C>A
  • NM_001318088.2:c.508C>A
  • NM_001365135.2:c.1297C>A
  • NP_000534.3:p.Pro477Thr
  • NP_001007594.2:p.Pro476Thr
  • NP_001305016.1:p.Pro477Thr
  • NP_001305017.1:p.Pro170Thr
  • NP_001352064.1:p.Pro433Thr
  • NC_000011.9:g.6415214C>A
  • NR_027400.3:n.1382C>A
  • NR_134502.2:n.901C>A
Protein change:
P170T
Links:
dbSNP: rs2134021440
NCBI 1000 Genomes Browser:
rs2134021440
Molecular consequence:
  • NM_000543.5:c.1429C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007593.3:c.1426C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318087.2:c.1429C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318088.2:c.508C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365135.2:c.1297C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.1382C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.901C>A - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001738432Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Apr 25, 2021) 		germlineresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedresearch

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 Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS, SCV001738432.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023