NM_000543.5(SMPD1):c.107_108delinsCT (p.Val36Ala) AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 28, 2023
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:: RCV001409612.7

Allele description [Variation Report for NM_000543.5(SMPD1):c.107_108delinsCT (p.Val36Ala)]

NM_000543.5(SMPD1):c.107_108delinsCT (p.Val36Ala)

Gene:

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

Variant type:

Indel

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.107_108delinsCT (p.Val36Ala)

HGVS:

NC_000011.10:g.6390705_6390706delinsCT
NG_011780.1:g.5281_5282delinsCT
NM_000543.5:c.107_108delinsCTMANE SELECT
NM_001007593.3:c.107_108delinsCT
NM_001318087.2:c.107_108delinsCT
NM_001318088.2:c.-855_-854delinsCT
NM_001365135.2:c.107_108delinsCT
NP_000534.3:p.Val36Ala
NP_001007594.2:p.Val36Ala
NP_001305016.1:p.Val36Ala
NP_001352064.1:p.Val36Ala
NC_000011.9:g.6411935_6411936delinsCT
NR_027400.3:n.232_233delinsCT
NR_134502.2:n.232_233delinsCT

Protein change:

V36A

Links:

dbSNP: rs2134005319

NCBI 1000 Genomes Browser:

rs2134005319

Molecular consequence:

NM_001318088.2:c.-855_-854delinsCT - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.107_108delinsCT - missense variant - [Sequence Ontology: SO:0001583]
NM_001007593.3:c.107_108delinsCT - missense variant - [Sequence Ontology: SO:0001583]
NM_001318087.2:c.107_108delinsCT - missense variant - [Sequence Ontology: SO:0001583]
NM_001365135.2:c.107_108delinsCT - missense variant - [Sequence Ontology: SO:0001583]
NR_027400.3:n.232_233delinsCT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.232_233delinsCT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Niemann-Pick disease, type B
Identifiers:: MONDO: MONDO:0011871; MedGen: C0268243; Orphanet: 77293; OMIM: 607616

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
SCV001611643	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Oct 28, 2023)	germline	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

SCV001611643

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Oct 28, 2023)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001611643.4

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

Last Updated: Sep 29, 2024

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