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NM_006772.3(SYNGAP1):c.490C>T (p.Arg164Ter) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Dec 6, 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:
RCV000412753.27

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.490C>T (p.Arg164Ter)]

NM_006772.3(SYNGAP1):c.490C>T (p.Arg164Ter)

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.490C>T (p.Arg164Ter)
HGVS:
  • NC_000006.12:g.33432787C>T
  • NG_016137.2:g.17718C>T
  • NM_001130066.2:c.490C>T
  • NM_006772.3:c.490C>TMANE SELECT
  • NP_001123538.1:p.Arg164Ter
  • NP_006763.2:p.Arg164Ter
  • LRG_1193t1:c.490C>T
  • LRG_1193:g.17718C>T
  • LRG_1193p1:p.Arg164Ter
  • NC_000006.11:g.33400564C>T
  • NM_006772.2:c.490C>T
Protein change:
R164*
Links:
dbSNP: rs1057518352
NCBI 1000 Genomes Browser:
rs1057518352
Molecular consequence:
  • NM_001130066.2:c.490C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006772.3:c.490C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
3

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000491912GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Dec 6, 2023) 		germlineclinical testing

Citation Link,

SCV001248668CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Pathogenic
(Jul 1, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000491912.5

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

Description

Identified in two siblings with developmental delay and seizures previously tested at GeneDx who inherited the variant from an unaffected parent who is mosaic; Nonsense variant predicted to result in protein truncation or nonsense mediated decay 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: 34800434, 30541864, 26989088, 28191889, 31031587, 28708303, 37583270)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001248668.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Oct 20, 2024