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NM_006772.3(SYNGAP1):c.509+1G>A AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 20, 2017
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:
RCV002316836.9

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.509+1G>A]

NM_006772.3(SYNGAP1):c.509+1G>A

Gene:
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.509+1G>A
HGVS:
  • NC_000006.12:g.33432807G>A
  • NG_016137.2:g.17738G>A
  • NM_001130066.2:c.509+1G>A
  • NM_006772.3:c.509+1G>AMANE SELECT
  • LRG_1193t1:c.509+1G>A
  • LRG_1193:g.17738G>A
  • NC_000006.11:g.33400584G>A
  • NM_006772.2:c.509+1G>A
Links:
dbSNP: rs1561781989
NCBI 1000 Genomes Browser:
rs1561781989
Molecular consequence:
  • NM_001130066.2:c.509+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_006772.3:c.509+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000850604Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Apr 20, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic and neurodevelopmental spectrum of SYNGAP1-associated intellectual disability and epilepsy.

Mignot C, von Stülpnagel C, Nava C, Ville D, Sanlaville D, Lesca G, Rastetter A, Gachet B, Marie Y, Korenke GC, Borggraefe I, Hoffmann-Zacharska D, Szczepanik E, Rudzka-Dybała M, Yiş U, Çağlayan H, Isapof A, Marey I, Panagiotakaki E, Korff C, Rossier E, Riess A, et al.

J Med Genet. 2016 Aug;53(8):511-22. doi: 10.1136/jmedgenet-2015-103451. Epub 2016 Mar 17. Erratum in: J Med Genet. 2016 Oct;53(10):720. doi: 10.1136/jmedgenet-2015-103451corr1.

PubMed [citation]
PMID:
26989088

Details of each submission

From Ambry Genetics, SCV000850604.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.509+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 5 of the SYNGAP1 gene. This alteration was detected as de novo in an individual with moderate intellectual disability (ID) (Mignot C et al. J. Med. Genet., 2016 Aug;53:511-22). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024