NM_012309.5(SHANK2):c.4906C>T (p.Arg1636Ter) AND Autism spectrum disorder

Clinical significance:Uncertain significance (Last evaluated: May 1, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001374606.1

Allele description [Variation Report for NM_012309.5(SHANK2):c.4906C>T (p.Arg1636Ter)]

NM_012309.5(SHANK2):c.4906C>T (p.Arg1636Ter)

Gene:
SHANK2:SH3 and multiple ankyrin repeat domains 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.3
Genomic location:
Preferred name:
NM_012309.5(SHANK2):c.4906C>T (p.Arg1636Ter)
HGVS:
  • NC_000011.10:g.70485387G>A
  • NG_042866.1:g.644410C>T
  • NM_001379226.1:c.3769C>T
  • NM_012309.4:c.4906C>T
  • NM_012309.5:c.4906C>TMANE SELECT
  • NM_133266.5:c.3142C>T
  • NM_133266.5:c.3142C>T
  • NP_001366155.1:p.Arg1257Ter
  • NP_036441.2:p.Arg1636Ter
  • NP_036441.2:p.Arg1636Ter
  • NP_573573.2:p.Arg1048Ter
  • NP_573573.2:p.Arg1048Ter
  • NC_000011.9:g.70331492G>A
  • NM_012309.3:c.4906C>T
Protein change:
R1048*
Links:
dbSNP: rs1565526121
NCBI 1000 Genomes Browser:
rs1565526121
Molecular consequence:
  • NM_001379226.1:c.3769C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_012309.4:c.4906C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_012309.5:c.4906C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_133266.5:c.3142C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Autism spectrum disorder
Synonyms:
Autism spectrum disorders; Autism susceptibility
Identifiers:
MONDO: MONDO:0005258; MeSH: D000067877; MedGen: C1510586; OMIM: PS209850

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001571451UNC Molecular Genetics Laboratory,University of North Carolina at Chapel Hill - CSER_NCGENEScriteria provided, single submitter
Uncertain significance
(May 1, 2020)
germlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedresearch

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 UNC Molecular Genetics Laboratory,University of North Carolina at Chapel Hill - CSER_NCGENES, SCV001571451.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)

Description

The SHANK2 c.4906C>T (p.Arg1636*) is a nonsense variant that is predicted to result in early protein truncation. However, this variant is located 74 nucleotides from the intron/exon junction of the penultimate exon of the SHANK2 gene and therefore may escape, or be subject to reduced nonsense-mediated RNA decay (NMD). This variant has not been reported previously in the medical literature or in human population variant databases such as gnomAD, and is considered a variant of uncertain clinical significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 25, 2021

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