NM_000543.5(SMPD1):c.1092-1G>C AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Nov 11, 2022
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:: RCV000177083.30

Allele description

NM_000543.5(SMPD1):c.1092-1G>C

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.1092-1G>C

HGVS:

NC_000011.10:g.6393215G>C
NG_011780.1:g.7791G>C
NG_029615.1:g.31200C>G
NM_000543.5:c.1092-1G>CMANE SELECT
NM_001007593.3:c.1089-1G>C
NM_001318087.2:c.1092-1G>C
NM_001318088.2:c.171-1G>C
NM_001365135.2:c.1132-402G>C
NC_000011.9:g.6414445G>C
NM_000543.4:c.1092-1G>C

Links:

dbSNP: rs398123474

NCBI 1000 Genomes Browser:

rs398123474

Molecular consequence:

NM_001365135.2:c.1132-402G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000543.5:c.1092-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001007593.3:c.1089-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001318087.2:c.1092-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001318088.2:c.171-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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cobalt ECF transporter T component CbiQ [Methanohalobium evestigatum]
cobalt ECF transporter T component CbiQ [Methanohalobium evestigatum]
gi|502960636|ref|WP_013195612.1|

Protein
mis18-binding protein 1 isoform X1 [Homo sapiens]
mis18-binding protein 1 isoform X1 [Homo sapiens]
gi|2217297903|ref|XP_047287502.1|

Protein
Mus musculus ariadne RBR E3 ubiquitin protein ligase 2 (Arih2), transcript varia...
Mus musculus ariadne RBR E3 ubiquitin protein ligase 2 (Arih2), transcript variant 2, mRNA
gi|2502273026|ref|NM_001357283.2|

Nucleotide
Mus musculus mitochondrial translation release factor in rescue (Mtrfr), transcr...
Mus musculus mitochondrial translation release factor in rescue (Mtrfr), transcript variant 1, mRNA; nuclear gene for mitochondrial product
gi|556695463|ref|NM_001134717.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000228903	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Jan 12, 2016)	germline	clinical testing	Citation Link,
SCV001249315	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jul 1, 2020)	germline	clinical testing	Citation Link,
SCV002601217	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000228903

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Jan 12, 2016)

germline

clinical testing

Citation Link,

SCV001249315

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jul 1, 2020)

germline

clinical testing

Citation Link,

SCV002601217

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 11, 2022)

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	yes	4	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	4	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000228903.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	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		4	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001249315.25

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	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	yes	not provided	not provided	not provided		4	not provided	not provided	not provided

From GeneDx, SCV002601217.2

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

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 26499107, 30795770, 8499909)

#	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: Oct 8, 2024

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