NM_001372044.2(SHANK3):c.1953dup (p.Arg652fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 13, 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:: RCV000599341.1

Allele description [Variation Report for NM_001372044.2(SHANK3):c.1953dup (p.Arg652fs)]

NM_001372044.2(SHANK3):c.1953dup (p.Arg652fs)

Genes:

LOC126863188:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:51142004-51143203 [Gene]
SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_001372044.2(SHANK3):c.1953dup (p.Arg652fs)

HGVS:

NC_000022.11:g.50704205dup
NG_070230.1:g.40070dup
NG_087684.2:g.730dup
NM_001372044.2:c.1953dupMANE SELECT
NP_001358973.1:p.Arg652fs
NC_000022.10:g.51142633dup
NM_033517.1:c.1728dupA

Protein change:

R652fs

Links:

dbSNP: rs1555908598

NCBI 1000 Genomes Browser:

rs1555908598

Molecular consequence:

NM_001372044.2:c.1953dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000710226	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Dec 13, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000710226

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Dec 13, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000710226.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1728dupA variant in the SHANK3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1728dupA variant causes a frameshift starting with codon Arginine 577, changes this amino acid to a Threonine residue, and creates a premature Stop codon at position 123 of the new reading frame, denoted p.Arg577ThrfsX123. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1728dupA variant is not observed in large population cohorts (Lek et al., 2016).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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