NM_003560.4(PLA2G6):c.1186+1G>A AND not provided

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

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Oct 23, 2023
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:: RCV001310807.24

Allele description

NM_003560.4(PLA2G6):c.1186+1G>A

Gene:

PLA2G6:phospholipase A2 group VI [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.1

Genomic location:

Preferred name:

NM_003560.4(PLA2G6):c.1186+1G>A

HGVS:

NC_000022.11:g.38129453C>T
NG_007094.3:g.90326G>A
NM_001004426.3:c.1186+1G>A
NM_001199562.3:c.1186+1G>A
NM_001349864.2:c.1186+1G>A
NM_001349865.2:c.1186+1G>A
NM_001349866.2:c.1186+1G>A
NM_001349867.2:c.652+1G>A
NM_001349868.2:c.508+1G>A
NM_001349869.2:c.652+1G>A
NM_003560.4:c.1186+1G>AMANE SELECT
LRG_1015t1:c.1186+1G>A
LRG_1015:g.90326G>A
NC_000022.10:g.38525460C>T
c.1186+1G>A

Links:

dbSNP: rs761815070

NCBI 1000 Genomes Browser:

rs761815070

Molecular consequence:

NM_001004426.3:c.1186+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001199562.3:c.1186+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349864.2:c.1186+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349865.2:c.1186+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349866.2:c.1186+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349867.2:c.652+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349868.2:c.508+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349869.2:c.652+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_003560.4:c.1186+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV001500748	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely pathogenic (Oct 1, 2020)	germline	clinical testing	Citation Link,
SCV001875287	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Oct 23, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001500748

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Likely pathogenic
(Oct 1, 2020)

germline

clinical testing

Citation Link,

SCV001875287

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Oct 23, 2023)

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	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001500748.20

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

From GeneDx, SCV001875287.4

#	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, 20584031, 32404165)

#	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: Jul 15, 2024

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