NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5]) AND Niemann-Pick disease, type A

Germline classification:: Benign (2 submissions)
Last evaluated:: Jul 15, 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:: RCV001808669.4

Allele description [Variation Report for NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5])]

NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5])

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5])

HGVS:

NC_000011.10:g.6390706GCTGGC[5]
NC_000011.9:g.6411936_6411941del
NG_011780.1:g.5282GCTGGC[5]
NM_000543.5:c.108GCTGGC[5]MANE SELECT
NM_001007593.3:c.108GCTGGC[5]
NM_001318087.2:c.108GCTGGC[5]
NM_001318088.2:c.-854GCTGGC[5]
NM_001365135.2:c.108GCTGGC[5]
NP_000534.3:p.38AL[5]
NP_001007594.2:p.38AL[5]
NP_001305016.1:p.38AL[5]
NP_001352064.1:p.38AL[5]
NC_000011.9:g.6411936GCTGGC[5]
NC_000011.9:g.6411936_6411941del
NC_000011.9:g.6411966_6411971delGCTGGC
NM_000543.4:c.120_125delGCTGGC
NM_000543.4:c.138_143del6
NM_000543.4:c.138_143delGCTGGC
NM_000543.5:c.138_143delMANE SELECT
NM_000543.5:c.138_143delGCTGGCMANE SELECT
NR_027400.3:n.233GCTGGC[5]
NR_134502.2:n.233GCTGGC[5]

Links:

dbSNP: rs3838786

NCBI 1000 Genomes Browser:

rs3838786

Molecular consequence:

NM_001318088.2:c.-854GCTGGC[5] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001007593.3:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318087.2:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001365135.2:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_027400.3:n.233GCTGGC[5] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.233GCTGGC[5] - 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

Recent activity

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PREDICTED: Homo sapiens zinc finger protein 772 (ZNF772), transcript variant X2,...
PREDICTED: Homo sapiens zinc finger protein 772 (ZNF772), transcript variant X2, mRNA
gi|2462565427|ref|XM_054321027.1|

Nucleotide
PREDICTED: Propithecus coquereli N-acetylneuraminate pyruvate lyase (dihydrodipi...
PREDICTED: Propithecus coquereli N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) (NPL), mRNA
gi|826281346|ref|XM_012639967.1|

Nucleotide
Cucumis melo cultivar AY chromosome 11, USDA_Cmelo_AY_1.0, whole genome shotgun ...
Cucumis melo cultivar AY chromosome 11, USDA_Cmelo_AY_1.0, whole genome shotgun sequence
gi|2313851673|gnl|ASM:GCF_025178375 1|ref|NC_066867.1||gpp|GPC_000014840.1||gnl|NCBI_GENOMES|127754

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002057493	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002091663	Natera, Inc.	no assertion criteria provided	Benign (May 15, 2017)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002057493

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 15, 2021)

germline

clinical testing

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

SCV002091663

Natera, Inc.

no assertion criteria provided

Benign
(May 15, 2017)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	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 Genome-Nilou Lab, SCV002057493.1

#	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	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002091663.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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