NM_000548.5(TSC2):c.5336A>G (p.Gln1779Arg) AND Tuberous sclerosis 2

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Aug 19, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000644420.5

Allele description [Variation Report for NM_000548.5(TSC2):c.5336A>G (p.Gln1779Arg)]

NM_000548.5(TSC2):c.5336A>G (p.Gln1779Arg)

Gene:
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.5336A>G (p.Gln1779Arg)
HGVS:
  • NC_000016.10:g.2088522A>G
  • NG_005895.1:g.44217A>G
  • NG_008617.1:g.54699T>C
  • NM_000548.5:c.5336A>GMANE SELECT
  • NM_001077183.2:c.5135A>G
  • NM_001114382.2:c.5267A>G
  • NM_001318827.1:c.5027A>G
  • NM_001318829.1:c.4991A>G
  • NM_001318831.1:c.4604A>G
  • NM_001318832.1:c.5168A>G
  • NM_001363528.1:c.5138A>G
  • NM_001370404.1:c.5204A>G
  • NM_001370405.1:c.5195A>G
  • NM_021055.2:c.5207A>G
  • NP_000539.2:p.Gln1779Arg
  • NP_001070651.1:p.Gln1712Arg
  • NP_001107854.1:p.Gln1756Arg
  • NP_001305756.1:p.Gln1676Arg
  • NP_001305758.1:p.Gln1664Arg
  • NP_001305760.1:p.Gln1535Arg
  • NP_001305761.1:p.Gln1723Arg
  • NP_001350457.1:p.Gln1713Arg
  • NP_001357333.1:p.Gln1735Arg
  • NP_001357334.1:p.Gln1732Arg
  • NP_066399.2:p.Gln1736Arg
  • LRG_487t1:c.5336A>G
  • LRG_487:g.44217A>G
  • NC_000016.9:g.2138523A>G
  • NM_000548.3:c.5336A>G
Protein change:
Q1535R
Links:
dbSNP: rs748947919
NCBI 1000 Genomes Browser:
rs748947919
Molecular consequence:
  • NM_000548.5:c.5336A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077183.2:c.5135A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114382.2:c.5267A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318827.1:c.5027A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318829.1:c.4991A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318831.1:c.4604A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318832.1:c.5168A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363528.1:c.5138A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370404.1:c.5204A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370405.1:c.5195A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021055.2:c.5207A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Tuberous sclerosis 2 (TSC2)
Identifiers:
MONDO: MONDO:0013199; MedGen: C1860707; Orphanet: 805; OMIM: 613254

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000766113Invitaecriteria provided, single submitter
Benign
(Apr 21, 2020)
germlineclinical testing

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

SCV000890947St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospitalcriteria provided, single submitter
Uncertain significance
(Aug 19, 2020)
germlineclinical testing

Citation Link

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000766113.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital, SCV000890947.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 14, 2021

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