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NM_000548.5(TSC2):c.3791del (p.Pro1264fs) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Apr 25, 2017
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000493012.2

Allele description [Variation Report for NM_000548.5(TSC2):c.3791del (p.Pro1264fs)]

NM_000548.5(TSC2):c.3791del (p.Pro1264fs)

Gene:
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.3791del (p.Pro1264fs)
HGVS:
  • NC_000016.10:g.2081775del
  • NC_000016.9:g.2131772del
  • NG_005895.1:g.37470del
  • NM_000548.5:c.3791delMANE SELECT
  • NM_001077183.3:c.3659del
  • NM_001114382.3:c.3791del
  • NM_001318827.2:c.3551del
  • NM_001318829.2:c.3515del
  • NM_001318831.2:c.3059del
  • NM_001318832.2:c.3692del
  • NM_001363528.2:c.3662del
  • NM_001370404.1:c.3659del
  • NM_001370405.1:c.3662del
  • NM_021055.3:c.3662del
  • NP_000539.2:p.Pro1264fs
  • NP_001070651.1:p.Pro1220fs
  • NP_001107854.1:p.Pro1264fs
  • NP_001305756.1:p.Pro1184fs
  • NP_001305758.1:p.Pro1172fs
  • NP_001305760.1:p.Pro1020fs
  • NP_001305761.1:p.Pro1231fs
  • NP_001350457.1:p.Pro1221fs
  • NP_001357333.1:p.Pro1220fs
  • NP_001357334.1:p.Pro1221fs
  • NP_066399.2:p.Pro1221fs
  • LRG_487t1:c.3791del
  • LRG_487:g.37470del
  • NC_000016.9:g.2131772del
  • NC_000016.9:g.2131772delC
  • NC_000016.9:g.2131776del
  • NM_000548.3:c.3791delC
  • p.Pro1264Leufs*61
  • p.(Pro1264Leufs*61)
Protein change:
P1020fs
Links:
Tuberous sclerosis database (TSC2): TSC2_00534; dbSNP: rs137854001
NCBI 1000 Genomes Browser:
rs137854001
Molecular consequence:
  • NM_000548.5:c.3791del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001077183.3:c.3659del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001114382.3:c.3791del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318827.2:c.3551del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318829.2:c.3515del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318831.2:c.3059del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318832.2:c.3692del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001363528.2:c.3662del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370404.1:c.3659del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370405.1:c.3662del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_021055.3:c.3662del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000581847GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Apr 25, 2017) 		germlineclinical testing

Citation Link,

SCV000615903Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)		Pathogenic
(Sep 21, 2016) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From GeneDx, SCV000581847.4

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

Description

The c.3791delC pathogenic variant in the TSC2 gene has been reported previously in association with TSC (TSC2 LOVD). The deletion causes a frameshift starting with codon Proline 1264, changes this amino acid to a Leucine residue and creates a premature Stop codon at position 61 of the new reading frame, denoted p.Pro1264LeufsX61. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3791delC variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server).

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

From Athena Diagnostics, SCV000615903.1

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

Last Updated: Sep 29, 2024