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NM_006772.3(SYNGAP1):c.1630C>T (p.Arg544Ter) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 31, 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:
RCV001092254.18

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.1630C>T (p.Arg544Ter)]

NM_006772.3(SYNGAP1):c.1630C>T (p.Arg544Ter)

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.1630C>T (p.Arg544Ter)
HGVS:
  • NC_000006.12:g.33438873C>T
  • NG_016137.2:g.23804C>T
  • NM_001130066.2:c.1630C>T
  • NM_006772.3:c.1630C>TMANE SELECT
  • NP_001123538.1:p.Arg544Ter
  • NP_006763.2:p.Arg544Ter
  • LRG_1193t1:c.1630C>T
  • LRG_1193:g.23804C>T
  • LRG_1193p1:p.Arg544Ter
  • NC_000006.11:g.33406650C>T
  • NM_006772.2:c.1630C>T
  • p.R544X
Protein change:
R544*
Links:
dbSNP: rs1554121443
NCBI 1000 Genomes Browser:
rs1554121443
Molecular consequence:
  • NM_001130066.2:c.1630C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006772.3:c.1630C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

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
SCV001248673CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Pathogenic
(Jan 1, 2020) 		germlineclinical testing

Citation Link,

SCV004170562GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Oct 31, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001248673.21

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV004170562.1

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

Description

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 in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31349857, 25326635, 26989088)

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

Last Updated: May 12, 2024