NM_000368.5(TSC1):c.2625+367A>G AND Tuberous sclerosis 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 3, 2023
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:: RCV000705549.10

Allele description [Variation Report for NM_000368.5(TSC1):c.2625+367A>G]

NM_000368.5(TSC1):c.2625+367A>G

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_000368.5(TSC1):c.2625+367A>G

HGVS:

NC_000009.12:g.132900348T>C
NG_012386.1:g.49286A>G
NM_000368.5:c.2625+367A>GMANE SELECT
NM_001162426.2:c.2622+367A>G
NM_001162427.2:c.2472+367A>G
NM_001362177.2:c.2262+367A>G
LRG_486t1:c.2625+367A>G
LRG_486:g.49286A>G
NC_000009.11:g.135775735T>C
NM_000368.4:c.2625+367A>G

Links:

dbSNP: rs1564474542

NCBI 1000 Genomes Browser:

rs1564474542

Molecular consequence:

NM_000368.5:c.2625+367A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001162426.2:c.2622+367A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001162427.2:c.2472+367A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001362177.2:c.2262+367A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Tuberous sclerosis 1 (TSC1)
Identifiers:: MONDO: MONDO:0008612; MedGen: C1854465; Orphanet: 805; OMIM: 191100

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000834550	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 3, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25927202, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000834550

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 3, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Targeted Next Generation Sequencing reveals previously unidentified TSC1 and TSC2 mutations.

Nellist M, Brouwer RW, Kockx CE, van Veghel-Plandsoen M, Withagen-Hermans C, Prins-Bakker L, Hoogeveen-Westerveld M, Mrsic A, van den Berg MM, Koopmans AE, de Wit MC, Jansen FE, Maat-Kievit AJ, van den Ouweland A, Halley D, de Klein A, van IJcken WF.

BMC Med Genet. 2015 Feb 25;16:10. doi: 10.1186/s12881-015-0155-4.

PubMed [citation]

PMID:: 25927202
PMCID:: PMC4422413

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000834550.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 581656). This variant has been observed in individuals with tuberous sclerosis complex (PMID: 25927202; Invitae). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 20 of the TSC1 gene. It does not directly change the encoded amino acid sequence of the TSC1 protein.

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

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine