NM_000368.5(TSC1):c.3112AGC[7] (p.Ser1043dup) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jul 1, 2024
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:: RCV000034610.24

Allele description [Variation Report for NM_000368.5(TSC1):c.3112AGC[7] (p.Ser1043dup)]

NM_000368.5(TSC1):c.3112AGC[7] (p.Ser1043dup)

Gene:

TSC1:TSC complex subunit 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_000368.5(TSC1):c.3112AGC[7] (p.Ser1043dup)

HGVS:

NC_000009.12:g.132896603TGC[7]
NG_012386.1:g.53016AGC[7]
NM_000368.5:c.3112AGC[7]MANE SELECT
NM_001162426.2:c.3109AGC[7]
NM_001162427.2:c.2959AGC[7]
NM_001362177.2:c.2749AGC[7]
NP_000359.1:p.Ser1043dup
NP_001155898.1:p.Ser1042dup
NP_001155899.1:p.Ser992dup
NP_001349106.1:p.Ser922dup
LRG_486:g.53016AGC[7]
NC_000009.11:g.135771987_135771988insGCT
NC_000009.11:g.135771990TGC[7]
NM_000368.3:c.3127_3129dup
NM_000368.4:c.3127_3129dupAGC
NM_000368.5:c.3127_3129dupMANE SELECT
NM_000368.5:c.3127_3129dupAGCMANE SELECT
p.Ser1043dup
p.(Ser1043dup)

Links:

Tuberous sclerosis database (TSC1): TSC1_00373; dbSNP: rs2234980

NCBI 1000 Genomes Browser:

rs2234980

Molecular consequence:

NM_000368.5:c.3112AGC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001162426.2:c.3109AGC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001162427.2:c.2959AGC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001362177.2:c.2749AGC[7] - inframe_insertion - [Sequence Ontology: SO:0001821]

Observations:

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
SCV000043506	Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq	no assertion criteria provided	probably not pathogenic (Jul 13, 2012)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV001860152	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link,
SCV002585094	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV004221393	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Aug 21, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11013456, 22703879, 26467025

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	1	not provided	not provided	342	not provided	research
not provided	germline	yes	15	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Two novel serine repeat length polymorphisms (1043insS and 1043insSS) at exon 23 of the TSC1 gene.

Pipo JR, Yamamoto T, Takeda H, Maegawa S, Nanba E, Ninomiya H, Ohno K, Takeshita K.

Hum Mutat. 2000 Oct;16(4):375. No abstract available.

PubMed [citation]

PMID:: 11013456

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.

Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG.

Am J Hum Genet. 2012 Jul 13;91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021. Epub 2012 Jun 14.

PubMed [citation]

PMID:: 22703879
PMCID:: PMC3397257

See all PubMed Citations (3)

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000043506.1

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

Description

The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See PubMed ID:22703879 for details.

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	342	not provided	discovery		1	not provided	not provided	not provided

From GeneDx, SCV001860152.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002585094.15

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	15	not provided	not provided	clinical testing	not provided

Description

TSC1: BS1

#	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		15	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004221393.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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

Last Updated: Oct 20, 2024

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