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NM_006950.3(SYN1):c.1663C>T (p.Gln555Ter) AND SYN1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 19, 2022
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:
RCV003407398.4

Allele description [Variation Report for NM_006950.3(SYN1):c.1663C>T (p.Gln555Ter)]

NM_006950.3(SYN1):c.1663C>T (p.Gln555Ter)

Gene:
SYN1:synapsin I [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.3
Genomic location:
Preferred name:
NM_006950.3(SYN1):c.1663C>T (p.Gln555Ter)
HGVS:
  • NC_000023.11:g.47574321G>A
  • NG_008437.1:g.50537C>T
  • NM_006950.3:c.1663C>TMANE SELECT
  • NM_133499.2:c.1663C>T
  • NP_008881.2:p.Gln555Ter
  • NP_598006.1:p.Gln555Ter
  • NC_000023.10:g.47433720G>A
Protein change:
Q555*; GLN555TER
Links:
OMIM: 313440.0002; dbSNP: rs397514679
NCBI 1000 Genomes Browser:
rs397514679
Molecular consequence:
  • NM_006950.3:c.1663C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_133499.2:c.1663C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
SYN1-related disorder
Synonyms:
SYN1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004114187PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 19, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004114187.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The SYN1 c.1663C>T variant is predicted to result in premature protein termination (p.Gln555*). This variant was reported in an individual with epilepsy (Fassio et al 2011. PubMed ID: 21441247; Lignani G et al 2013. PubMed ID: 23406870; Nguyen DK et al 2015. PubMed ID: 26096837; Cabana JF et al 2018. PubMed ID: 29671924). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in SYN1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: May 19, 2024