NM_001372044.2(SHANK3):c.3760A>T (p.Lys1254Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 6, 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:: RCV000522491.1

Allele description [Variation Report for NM_001372044.2(SHANK3):c.3760A>T (p.Lys1254Ter)]

NM_001372044.2(SHANK3):c.3760A>T (p.Lys1254Ter)

Gene:

SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_001372044.2(SHANK3):c.3760A>T (p.Lys1254Ter)

HGVS:

NC_000022.11:g.50721368A>T
NG_070230.1:g.57152A>T
NM_001372044.2:c.3760A>TMANE SELECT
NM_033517.1:c.3535A>T
NP_001358973.1:p.Lys1254Ter
NP_277052.1:p.Lys1179Ter
NC_000022.10:g.51159796A>T

Protein change:

K1179*

Links:

dbSNP: rs771528741

NCBI 1000 Genomes Browser:

rs771528741

Molecular consequence:

NM_001372044.2:c.3760A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033517.1:c.3535A>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000621316	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Oct 6, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000621316

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Oct 6, 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, SCV000621316.2

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

Description

The K1179X variant in the SHANK3 gene has not been reported previously as a pathogenic variantnor 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 K1179X variant is not observed in large population cohorts (Lek et al., 2016). We interpret K1179X as a pathogenic variant.

#	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: Oct 8, 2024

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