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NM_012309.4(SHANK2):c.4906C>T (p.Arg1636Ter)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Apr 16, 2021)
Last evaluated:
May 1, 2020
Accession:
VCV000620503.3
Variation ID:
620503
Description:
single nucleotide variant
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NM_012309.4(SHANK2):c.4906C>T (p.Arg1636Ter)

Allele ID
611755
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.3
Genomic location
11: 70485387 (GRCh38) GRCh38 UCSC
11: 70331492 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.70485387G>A
NC_000011.9:g.70331492G>A
NG_042866.1:g.644410C>T
... more HGVS
Protein change
R1636*, R1048*
Other names
-
Canonical SPDI
NC_000011.10:70485386:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs1565526121
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Dec 20, 2018 RCV000760886.1
Uncertain significance 1 criteria provided, single submitter May 1, 2020 RCV001374606.1
Likely pathogenic 1 no assertion criteria provided Feb 5, 2020 RCV001028010.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SHANK2 Some evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
173 185

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 20, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000890782.1
Submitted: (Mar 13, 2019)
Evidence details
Comment:
The R1636X variant in the SHANK2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This … (more)
Uncertain significance
(May 01, 2020)
criteria provided, single submitter
Method: research
Autism spectrum disorder
Allele origin: germline
UNC Molecular Genetics Laboratory,University of North Carolina at Chapel Hill
Study: CSER_NCGENES
Accession: SCV001571451.1
Submitted: (Apr 16, 2021)
Evidence details
Comment:
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 … (more)
Likely pathogenic
(Feb 05, 2020)
no assertion criteria provided
Method: clinical testing
Autism 17
Allele origin: germline
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City
Accession: SCV001190774.1
Submitted: (Feb 12, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1565526121...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 02, 2021