NM_000543.5(SMPD1):c.1644delinsAA (p.Asn549fs) AND Niemann-Pick disease, type A

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 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:: RCV000666041.2

Allele description [Variation Report for NM_000543.5(SMPD1):c.1644delinsAA (p.Asn549fs)]

NM_000543.5(SMPD1):c.1644delinsAA (p.Asn549fs)

Gene:

SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.1644delinsAA (p.Asn549fs)

HGVS:

NC_000011.10:g.6394355delinsAA
NG_011780.1:g.8931delinsAA
NG_029615.1:g.30060delinsTT
NM_000543.5:c.1644delinsAAMANE SELECT
NM_001007593.3:c.1641delinsAA
NM_001318087.2:c.*137delinsAA
NM_001318088.2:c.723delinsAA
NM_001365135.2:c.1512delinsAA
NP_000534.3:p.Asn549fs
NP_001007594.2:p.Asn548fs
NP_001305017.1:p.Asn242fs
NP_001352064.1:p.Asn505fs
NC_000011.9:g.6415585delinsAA
NM_000543.4:c.1644delCinsAA
NR_027400.3:n.1597delinsAA
NR_134502.2:n.1136delinsAA

Protein change:

N242fs

Links:

dbSNP: rs1554935600

NCBI 1000 Genomes Browser:

rs1554935600

Molecular consequence:

NM_001318087.2:c.*137delinsAA - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000543.5:c.1644delinsAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001007593.3:c.1641delinsAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318088.2:c.723delinsAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365135.2:c.1512delinsAA - frameshift variant - [Sequence Ontology: SO:0001589]
NR_027400.3:n.1597delinsAA - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.1136delinsAA - 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
SCV000790274	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Mar 23, 2017)	unknown	clinical testing	Citation Link,
SCV005052852	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 11, 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

SCV000790274

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Mar 23, 2017)

unknown

clinical testing

Citation Link,

SCV005052852

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 11, 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

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 Counsyl, SCV000790274.1

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

#	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

From Baylor Genetics, SCV005052852.1

#	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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