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NM_006772.3(SYNGAP1):c.1513T>G (p.Tyr505Asp) AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 1, 2023
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:
RCV004463682.1

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.1513T>G (p.Tyr505Asp)]

NM_006772.3(SYNGAP1):c.1513T>G (p.Tyr505Asp)

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.1513T>G (p.Tyr505Asp)
HGVS:
  • NC_000006.12:g.33438545T>G
  • NG_016137.2:g.23476T>G
  • NM_001130066.2:c.1513T>G
  • NM_006772.3:c.1513T>GMANE SELECT
  • NP_001123538.1:p.Tyr505Asp
  • NP_006763.2:p.Tyr505Asp
  • LRG_1193t1:c.1513T>G
  • LRG_1193:g.23476T>G
  • LRG_1193p1:p.Tyr505Asp
  • NC_000006.11:g.33406322T>G
  • NM_006772.2:c.1513T>G
Protein change:
Y505D
Molecular consequence:
  • NM_001130066.2:c.1513T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006772.3:c.1513T>G - 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
SCV004961435Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Nov 1, 2023) 		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, SCV004961435.1

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

Description

The c.1513T>G (p.Y505D) alteration is located in exon 9 (coding exon 9) of the SYNGAP1 gene. This alteration results from a T to G substitution at nucleotide position 1513, causing the tyrosine (Y) at amino acid position 505 to be replaced by an aspartic acid (D). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. This missense alteration is located in a region that has a low rate of benign missense variation (Lek, 2016; Firth, 2009). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as likely pathogenic.

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

Last Updated: May 7, 2024