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NM_000368.5(TSC1):c.1983C>T (p.Ser661=) AND Tuberous sclerosis 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 29, 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:
RCV002627770.2

Allele description

NM_000368.5(TSC1):c.1983C>T (p.Ser661=)

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.1983C>T (p.Ser661=)
HGVS:
  • NC_000009.12:g.132905595G>A
  • NG_012386.1:g.44039C>T
  • NM_000368.5:c.1983C>TMANE SELECT
  • NM_001162426.2:c.1980C>T
  • NM_001162427.2:c.1830C>T
  • NM_001362177.2:c.1620C>T
  • NM_001406592.1:c.1983C>T
  • NM_001406593.1:c.1983C>T
  • NM_001406594.1:c.1983C>T
  • NM_001406595.1:c.1983C>T
  • NM_001406596.1:c.1983C>T
  • NM_001406597.1:c.1980C>T
  • NM_001406598.1:c.1980C>T
  • NM_001406599.1:c.1980C>T
  • NM_001406600.1:c.1980C>T
  • NM_001406601.1:c.1983C>T
  • NM_001406602.1:c.1983C>T
  • NM_001406603.1:c.1980C>T
  • NM_001406604.1:c.1980C>T
  • NM_001406605.1:c.1983C>T
  • NM_001406606.1:c.1983C>T
  • NM_001406607.1:c.1983C>T
  • NM_001406608.1:c.1980C>T
  • NM_001406609.1:c.1980C>T
  • NM_001406610.1:c.1830C>T
  • NM_001406611.1:c.1827C>T
  • NM_001406612.1:c.1827C>T
  • NM_001406613.1:c.1827C>T
  • NM_001406614.1:c.1620C>T
  • NM_001406615.1:c.1620C>T
  • NM_001406616.1:c.1620C>T
  • NM_001406617.1:c.1620C>T
  • NM_001406618.1:c.1620C>T
  • NM_001406619.1:c.1620C>T
  • NM_001406620.1:c.1617C>T
  • NM_001406621.1:c.1617C>T
  • NM_001406622.1:c.1617C>T
  • NM_001406623.1:c.1617C>T
  • NM_001406624.1:c.1620C>T
  • NM_001406625.1:c.1617C>T
  • NM_001406626.1:c.1032C>T
  • NM_001406627.1:c.1029C>T
  • NM_001406628.1:c.1029C>T
  • NM_001406629.1:c.930C>T
  • NM_001406630.1:c.930C>T
  • NP_000359.1:p.Ser661=
  • NP_000359.1:p.Ser661=
  • NP_000359.1:p.Ser661=
  • NP_001155898.1:p.Ser660=
  • NP_001155899.1:p.Ser610=
  • NP_001349106.1:p.Ser540=
  • NP_001393521.1:p.Ser661=
  • NP_001393522.1:p.Ser661=
  • NP_001393523.1:p.Ser661=
  • NP_001393524.1:p.Ser661=
  • NP_001393525.1:p.Ser661=
  • NP_001393526.1:p.Ser660=
  • NP_001393527.1:p.Ser660=
  • NP_001393528.1:p.Ser660=
  • NP_001393529.1:p.Ser660=
  • NP_001393530.1:p.Ser661=
  • NP_001393531.1:p.Ser661=
  • NP_001393532.1:p.Ser660=
  • NP_001393533.1:p.Ser660=
  • NP_001393534.1:p.Ser661=
  • NP_001393535.1:p.Ser661=
  • NP_001393536.1:p.Ser661=
  • NP_001393537.1:p.Ser660=
  • NP_001393538.1:p.Ser660=
  • NP_001393539.1:p.Ser610=
  • NP_001393540.1:p.Ser609=
  • NP_001393541.1:p.Ser609=
  • NP_001393542.1:p.Ser609=
  • NP_001393543.1:p.Ser540=
  • NP_001393544.1:p.Ser540=
  • NP_001393545.1:p.Ser540=
  • NP_001393546.1:p.Ser540=
  • NP_001393547.1:p.Ser540=
  • NP_001393548.1:p.Ser540=
  • NP_001393549.1:p.Ser539=
  • NP_001393550.1:p.Ser539=
  • NP_001393551.1:p.Ser539=
  • NP_001393552.1:p.Ser539=
  • NP_001393553.1:p.Ser540=
  • NP_001393554.1:p.Ser539=
  • NP_001393555.1:p.Ser344=
  • NP_001393556.1:p.Ser343=
  • NP_001393557.1:p.Ser343=
  • NP_001393558.1:p.Ser310=
  • NP_001393559.1:p.Ser310=
  • LRG_486t1:c.1983C>T
  • LRG_486:g.44039C>T
  • LRG_486p1:p.Ser661=
  • NC_000009.11:g.135780982G>A
  • NM_000368.3:c.1983C>T
  • NM_000368.4:c.1983C>T
  • NR_176214.1:n.2200C>T
  • NR_176215.1:n.2200C>T
  • NR_176216.1:n.2067C>T
  • NR_176217.1:n.2197C>T
  • NR_176218.1:n.2200C>T
Molecular consequence:
  • NR_176214.1:n.2200C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176215.1:n.2200C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176216.1:n.2067C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176217.1:n.2197C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176218.1:n.2200C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000368.5:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001162426.2:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001162427.2:c.1830C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362177.2:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406592.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406593.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406594.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406595.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406596.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406597.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406598.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406599.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406600.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406601.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406602.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406603.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406604.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406605.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406606.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406607.1:c.1983C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406608.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406609.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406610.1:c.1830C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406611.1:c.1827C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406612.1:c.1827C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406613.1:c.1827C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406614.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406615.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406616.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406617.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406618.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406619.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406620.1:c.1617C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406621.1:c.1617C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406622.1:c.1617C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406623.1:c.1617C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406624.1:c.1620C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406625.1:c.1617C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406626.1:c.1032C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406627.1:c.1029C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406628.1:c.1029C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406629.1:c.930C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406630.1:c.930C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002972662Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 29, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 Invitae, SCV002972662.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change affects codon 661 of the TSC1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the TSC1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1937855). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 11, 2024