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NM_006772.3(SYNGAP1):c.2596G>A (p.Val866Ile) AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 1, 2016
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:
RCV002317404.9

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.2596G>A (p.Val866Ile)]

NM_006772.3(SYNGAP1):c.2596G>A (p.Val866Ile)

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.2596G>A (p.Val866Ile)
HGVS:
  • NC_000006.12:g.33443148G>A
  • NG_016137.2:g.28079G>A
  • NM_001130066.2:c.2554G>A
  • NM_006772.3:c.2596G>AMANE SELECT
  • NP_001123538.1:p.Val852Ile
  • NP_006763.2:p.Val866Ile
  • LRG_1193t1:c.2596G>A
  • LRG_1193:g.28079G>A
  • LRG_1193p1:p.Val866Ile
  • NC_000006.11:g.33410925G>A
  • NM_006772.2:c.2596G>A
Protein change:
V852I
Links:
dbSNP: rs768878991
NCBI 1000 Genomes Browser:
rs768878991
Molecular consequence:
  • NM_001130066.2:c.2554G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006772.3:c.2596G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000851217Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Sep 1, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000851217.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.V866I variant (also known as c.2596G>A), located in coding exon 15 of the SYNGAP1 gene, results from a G to A substitution at nucleotide position 2596. The valine at codon 866 is replaced by isoleucine, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.

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

Last Updated: Nov 3, 2024