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NM_001372044.2(SHANK3):c.3989_4001del (p.Arg1330fs) AND not provided

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Jun 9, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000269712.24

Allele description

NM_001372044.2(SHANK3):c.3989_4001del (p.Arg1330fs)

Gene:
SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_001372044.2(SHANK3):c.3989_4001del (p.Arg1330fs)
Other names:
NM_001080420.1:c.3812_3824del
HGVS:
  • NC_000022.11:g.50721597_50721609del
  • NG_070230.1:g.57381_57393del
  • NM_001372044.2:c.3989_4001delMANE SELECT
  • NM_033517.1:c.3764_3776del
  • NP_001358973.1:p.Arg1330fs
  • NP_277052.1:p.Arg1255Leufs
  • NP_277052.1:p.Arg1255fs
  • NC_000022.10:g.51160025_51160037del
  • NM_033517.1:c.3764_3776del13
  • NM_033517.1:c.3764_3776delGGGCCCAGCCCCC
Protein change:
R1255fs
Links:
dbSNP: rs886041238
NCBI 1000 Genomes Browser:
rs886041238
Molecular consequence:
  • NM_001372044.2:c.3989_4001del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_033517.1:c.3764_3776del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000329517GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Jun 9, 2022)
germlineclinical testing

Citation Link,

SCV001448080Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 23, 2020)
germlineclinical testing

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

SCV001500270CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Jan 1, 2021)
germlineclinical testing

Citation Link,

SCV004031368Molecular Genetics laboratory, Necker Hospital
no assertion criteria provided
Pathogenic
(Apr 20, 2021)
de novoclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes1not providednot provided1not 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 GeneDx, SCV000329517.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25188300, 29719671, 28135719)

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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001448080.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001500270.17

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Molecular Genetics laboratory, Necker Hospital, SCV004031368.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024