NM_000543.5(SMPD1):c.785_807del (p.Leu262fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 9, 2020
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:: RCV000175621.6

Allele description [Variation Report for NM_000543.5(SMPD1):c.785_807del (p.Leu262fs)]

NM_000543.5(SMPD1):c.785_807del (p.Leu262fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.785_807del (p.Leu262fs)

HGVS:

NC_000011.10:g.6391850_6391872del
NG_011780.1:g.6426_6448del
NM_000543.5:c.785_807delMANE SELECT
NM_001007593.3:c.782_804del
NM_001318087.2:c.785_807del
NM_001318088.2:c.-177_-155del
NM_001365135.2:c.785_807del
NP_000534.3:p.Leu262fs
NP_001007594.2:p.Leu261fs
NP_001305016.1:p.Leu262fs
NP_001352064.1:p.Leu262fs
NC_000011.10:g.6391850_6391872del23
NC_000011.9:g.6413076_6413098del
NC_000011.9:g.6413080_6413102del
NM_000543.4(SMPD1):c.785_807del23
NM_000543.4:c.785_807del
NM_000543.4:c.785_807del23
NM_000543.4:c.785_807delTGTTGAGTGGGCTGGGCCCAGCC
NR_027400.3:n.910_932del
p.Leu262Argfs

Protein change:

L261fs

Links:

dbSNP: rs794727252

NCBI 1000 Genomes Browser:

rs794727252

Molecular consequence:

NM_001318088.2:c.-177_-155del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.785_807del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001007593.3:c.782_804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318087.2:c.785_807del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365135.2:c.785_807del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_027400.3:n.910_932del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000227145	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV001767818	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 9, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000227145

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV001767818

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 9, 2020)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000227145.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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		3	not provided	not provided	not provided

From GeneDx, SCV001767818.1

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

Description

Has not been previously published as pathogenic or benign to our knowledge; Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 23418865)

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

Last Updated: Sep 29, 2024

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