NM_000368.5(TSC1):c.2509_2512del (p.Asn837fs) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 19, 2024
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:: RCV000522266.8

Allele description [Variation Report for NM_000368.5(TSC1):c.2509_2512del (p.Asn837fs)]

NM_000368.5(TSC1):c.2509_2512del (p.Asn837fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_000368.5(TSC1):c.2509_2512del (p.Asn837fs)

HGVS:

NC_000009.12:g.132900830_132900833del
NG_012386.1:g.48803_48806del
NM_000368.5:c.2509_2512delMANE SELECT
NM_001162426.2:c.2506_2509del
NM_001162427.2:c.2356_2359del
NM_001362177.2:c.2146_2149del
NP_000359.1:p.Asn837fs
NP_001155898.1:p.Asn836fs
NP_001155899.1:p.Asn786fs
NP_001349106.1:p.Asn716fs
LRG_486:g.48803_48806del
NC_000009.11:g.135776215_135776218del
NC_000009.11:g.135776217_135776220del
NM_000368.3:c.2509_2512del
NM_000368.4:c.2509_2512delAACA
NM_000368.5:c.2509_2512del
NM_000368.5:c.2509_2512delAACAMANE SELECT
p.(Asn837Valfs*11)

Protein change:

N716fs

Links:

Tuberous sclerosis database (TSC1): TSC1_00170; Tuberous sclerosis database (TSC1): TSC1_00233; dbSNP: rs118203707

NCBI 1000 Genomes Browser:

rs118203707

Molecular consequence:

NM_000368.5:c.2509_2512del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001162426.2:c.2506_2509del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001162427.2:c.2356_2359del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001362177.2:c.2146_2149del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Rattus norvegicus diacylglycerol kinase, eta (Dgkh), transcript varia...
PREDICTED: Rattus norvegicus diacylglycerol kinase, eta (Dgkh), transcript variant X1, mRNA
gi|2678899693|ref|XM_039094035.2|

Nucleotide
RecName: Full=Probable histone H2A.7; AltName: Full=HTA6
RecName: Full=Probable histone H2A.7; AltName: Full=HTA6
gi|75309136|sp|Q9FJE8.1|H2A7_ARATH

Protein
rhodopsin [Tursiops truncatus]
rhodopsin [Tursiops truncatus]
gi|525507094|ref|NP_001267588.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000617401	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 19, 2024)	germline	clinical testing	Citation Link,
SCV001807275	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001974546	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000617401

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 19, 2024)

germline

clinical testing

Citation Link,

SCV001807275

Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus

no assertion criteria provided

Pathogenic

germline

clinical testing

SCV001974546

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

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, SCV000617401.5

#	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: 14756965, 18032745, 15798777, 9924605, 17304050, 10227394, 10363127, 11112665, 32917966, 35253369, 31598950, 29286531, 32211034, 12015165)

#	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 Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001807275.1

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001974546.1

#	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

Last Updated: Sep 29, 2024

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