NM_000543.5(SMPD1):c.1598C>A (p.Pro533Gln) AND Niemann-Pick disease, type A

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Mar 28, 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:: RCV001527432.4

Allele description [Variation Report for NM_000543.5(SMPD1):c.1598C>A (p.Pro533Gln)]

NM_000543.5(SMPD1):c.1598C>A (p.Pro533Gln)

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.1598C>A (p.Pro533Gln)

HGVS:

NC_000011.10:g.6394309C>A
NG_011780.1:g.8885C>A
NG_029615.1:g.30106G>T
NM_000543.5:c.1598C>AMANE SELECT
NM_001007593.3:c.1595C>A
NM_001318087.2:c.*91C>A
NM_001318088.2:c.677C>A
NM_001365135.2:c.1466C>A
NP_000534.3:p.Pro533Gln
NP_001007594.2:p.Pro532Gln
NP_001305017.1:p.Pro226Gln
NP_001352064.1:p.Pro489Gln
NC_000011.9:g.6415539C>A
NR_027400.3:n.1551C>A
NR_134502.2:n.1090C>A

Protein change:

P226Q

Links:

dbSNP: rs199915216

NCBI 1000 Genomes Browser:

rs199915216

Molecular consequence:

NM_001318087.2:c.*91C>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000543.5:c.1598C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001007593.3:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318088.2:c.677C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365135.2:c.1466C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_027400.3:n.1551C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.1090C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001738437	Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 25, 2021)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV004203211	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 28, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001738437

Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 25, 2021)

germline

research

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

SCV004203211

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 28, 2024)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	not provided	research

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, SCV001738437.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Baylor Genetics, SCV004203211.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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