NM_006772.3(SYNGAP1):c.3583-6G>A AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 27, 2024
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:: RCV001778797.4

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.3583-6G>A]

NM_006772.3(SYNGAP1):c.3583-6G>A

Genes:

SYNGAP1-AS1:SYNGAP1 antisense RNA 1 [Gene - HGNC]
SYNGAP1:synaptic Ras GTPase activating protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.32

Genomic location:

Preferred name:

NM_006772.3(SYNGAP1):c.3583-6G>A

HGVS:

NC_000006.12:g.33446569G>A
NG_016137.2:g.31500G>A
NM_001130066.2:c.3541-12G>A
NM_006772.3:c.3583-6G>AMANE SELECT
LRG_1193t1:c.3583-6G>A
LRG_1193:g.31500G>A
NC_000006.11:g.33414346G>A
NM_006772.2:c.3583-6G>A
g.33414346G>A

Links:

dbSNP: rs869312674

NCBI 1000 Genomes Browser:

rs869312674

Molecular consequence:

NM_001130066.2:c.3541-12G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_006772.3:c.3583-6G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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protein Wnt-6 precursor [Mus musculus]
protein Wnt-6 precursor [Mus musculus]
gi|34328158|ref|NP_033552.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002015747	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 27, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002015747

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Feb 27, 2024)

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV002015747.3

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 28524815, 28721930, 25167861, 28554332, 33639450, 34070602)

#	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: Nov 3, 2024

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