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NM_006772.3(SYNGAP1):c.3227del (p.Gln1075_Leu1076insTer) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 3, 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:
RCV000481505.1

Allele description [Variation Report for NM_006772.3(SYNGAP1):c.3227del (p.Gln1075_Leu1076insTer)]

NM_006772.3(SYNGAP1):c.3227del (p.Gln1075_Leu1076insTer)

Genes:
SYNGAP1-AS1:SYNGAP1 antisense RNA 1 [Gene - HGNC]
SYNGAP1:synaptic Ras GTPase activating protein 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6p21.32
Genomic location:
Preferred name:
NM_006772.3(SYNGAP1):c.3227del (p.Gln1075_Leu1076insTer)
HGVS:
  • NC_000006.12:g.33443779del
  • NG_016137.2:g.28710del
  • NM_001130066.2:c.3185del
  • NM_006772.3:c.3227delMANE SELECT
  • NP_001123538.1:p.Gln1061_Leu1062insTer
  • NP_006763.2:p.Gln1075_Leu1076insTer
  • LRG_1193t1:c.3227del
  • LRG_1193:g.28710del
  • LRG_1193p1:p.Gln1075_Leu1076insTer
  • NC_000006.11:g.33411556del
  • NM_006772.2:c.3227delT
Links:
dbSNP: rs1064796033
NCBI 1000 Genomes Browser:
rs1064796033
Molecular consequence:
  • NM_001130066.2:c.3185del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006772.3:c.3227del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000572406GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jan 3, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000572406.4

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

Description

The L1076X pathogenic variant in the SYNGAP1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The L1076X variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret L1076X as a pathogenic variant.

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

Last Updated: Apr 23, 2022