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

This record was updated by the submitter. Please see the current version.

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:: RCV000269712.29

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:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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aldehyde dehydrogenase family 3 member B1 isoform X2 [Papio anubis]
aldehyde dehydrogenase family 3 member B1 isoform X2 [Papio anubis]
gi|685584905|ref|XP_009183753.1|

Protein
Scopelarchus stephensi voucher SIO 10-174 cytochrome oxidase subunit I (COI) gen...
Scopelarchus stephensi voucher SIO 10-174 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
gi|764145418|gb|KM983050.1|

Nucleotide
RecName: Full=Sporulation-regulated protein 3
RecName: Full=Sporulation-regulated protein 3
gi|1174429|sp|P41901.1|SPR3_YEAST

Protein
Protein Links for PopSet (Select 213520526) (34)
Protein
MAG: Hyphomicrobium sp. isolate SF1_2_26, whole genome shotgun sequencing projec...
MAG: Hyphomicrobium sp. isolate SF1_2_26, whole genome shotgun sequencing project
gi|2739910231|gb|JBEBIO000000000.1| O010000000

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329517	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 9, 2022)	germline	clinical testing	Citation Link,
SCV001448080	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001500270	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jan 1, 2021)	germline	clinical testing	Citation Link,
SCV004031368	Molecular Genetics laboratory, Necker Hospital	no assertion criteria provided	Pathogenic (Apr 20, 2021)	de novo	clinical testing

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical 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

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

#	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

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

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

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

From CeGaT Center for Human Genetics Tuebingen, SCV001500270.21

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

#	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		1	not provided	not provided	not provided

From Molecular Genetics laboratory, Necker Hospital, SCV004031368.1

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

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

Last Updated: Sep 1, 2024

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