NM_003073.5(SMARCB1):c.1066_1067del (p.Leu356fs) AND Intellectual disability, autosomal dominant 15

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 17, 2022
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:: RCV002279725.1

Allele description [Variation Report for NM_003073.5(SMARCB1):c.1066_1067del (p.Leu356fs)]

NM_003073.5(SMARCB1):c.1066_1067del (p.Leu356fs)

Gene:

SMARCB1:SWI/SNF related BAF chromatin remodeling complex subunit B1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

22q11.23

Genomic location:

Preferred name:

NM_003073.5(SMARCB1):c.1066_1067del (p.Leu356fs)

HGVS:

NC_000022.10:g.24175836_24175837del
NC_000022.11:g.23833649CT[1]
NG_009303.1:g.51687CT[1]
NM_001007468.3:c.1039_1040del
NM_001317946.2:c.1093_1094del
NM_001362877.2:c.1120_1121del
NM_003073.5:c.1066_1067delMANE SELECT
NP_001007469.1:p.Leu347fs
NP_001304875.1:p.Leu365fs
NP_001349806.1:p.Leu374fs
NP_003064.2:p.Leu356fs
LRG_520t1:c.1066_1067del
LRG_520:g.51687CT[1]
NC_000022.10:g.24175836CT[1]
NC_000022.10:g.24175836_24175837del
NC_000022.10:g.24175836_24175837delCT
NM_003073.3:c.1066_1067delCT
NM_003073.4:c.1066_1067del

Protein change:

L347fs

Links:

dbSNP: rs1555881563

NCBI 1000 Genomes Browser:

rs1555881563

Molecular consequence:

NM_001007468.3:c.1039_1040del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001317946.2:c.1093_1094del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001362877.2:c.1120_1121del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003073.5:c.1066_1067del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Intellectual disability, autosomal dominant 15 (CSS3)
Synonyms:: COFFIN-SIRIS SYNDROME 3
Identifiers:: MONDO: MONDO:0013820; MedGen: C3553248; Orphanet: 1465; OMIM: 614608

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002562255	Laboratory Division, Turku University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 17, 2022)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002562255

Laboratory Division, Turku University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 17, 2022)

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	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 Laboratory Division, Turku University Hospital, SCV002562255.1

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

Description

ACMG class 5: pathogenic (PVS1, PS2, PM2). Variant was absent from parents indicating a de novo origin. The discovered SMARCB1-variant was rare as it was not reported in the Genome Aggregation Database (GnomAD) or in literature. However, this variant was recently reported in Clinical Variant Database as a likely pathogenic variant (ClinVar: VCV000532963.5)

#	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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine