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NM_000548.5(TSC2):c.3799C>T (p.Pro1267Ser) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 12, 2017
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:
RCV000521160.1

Allele description [Variation Report for NM_000548.5(TSC2):c.3799C>T (p.Pro1267Ser)]

NM_000548.5(TSC2):c.3799C>T (p.Pro1267Ser)

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.3799C>T (p.Pro1267Ser)
HGVS:
  • NC_000016.10:g.2081783C>T
  • NG_005895.1:g.37478C>T
  • NM_000548.5:c.3799C>TMANE SELECT
  • NM_001077183.3:c.3667C>T
  • NM_001114382.3:c.3799C>T
  • NM_001318827.2:c.3559C>T
  • NM_001318829.2:c.3523C>T
  • NM_001318831.2:c.3067C>T
  • NM_001318832.2:c.3700C>T
  • NM_001363528.2:c.3670C>T
  • NM_001370404.1:c.3667C>T
  • NM_001370405.1:c.3670C>T
  • NM_021055.3:c.3670C>T
  • NP_000539.2:p.Pro1267Ser
  • NP_001070651.1:p.Pro1223Ser
  • NP_001107854.1:p.Pro1267Ser
  • NP_001305756.1:p.Pro1187Ser
  • NP_001305758.1:p.Pro1175Ser
  • NP_001305760.1:p.Pro1023Ser
  • NP_001305761.1:p.Pro1234Ser
  • NP_001350457.1:p.Pro1224Ser
  • NP_001357333.1:p.Pro1223Ser
  • NP_001357334.1:p.Pro1224Ser
  • NP_066399.2:p.Pro1224Ser
  • LRG_487t1:c.3799C>T
  • LRG_487:g.37478C>T
  • NC_000016.9:g.2131784C>T
  • NM_000548.3:c.3799C>T
Protein change:
P1023S
Links:
dbSNP: rs757010959
NCBI 1000 Genomes Browser:
rs757010959
Molecular consequence:
  • NM_000548.5:c.3799C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077183.3:c.3667C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114382.3:c.3799C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318827.2:c.3559C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318829.2:c.3523C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318831.2:c.3067C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318832.2:c.3700C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363528.2:c.3670C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370404.1:c.3667C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370405.1:c.3670C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021055.3:c.3670C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000621504GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Oct 12, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000621504.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the TSC2 gene. The P1267S variant has notbeen published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The P1267S variant is observed in 2/245,356 (0.0008%) alleles in large population cohorts (Lek el al., 2016). The P1267S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved, and in silico analysis predicts this variant likely does not alter the protein structure/function. Additionally, this substitution does not occur within known functional domains of the tuberin protein, where many pathogenic missense variants have been identified (Northrup et al., 2011; Au et al., 2007). Therefore, based onthe currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: May 7, 2024