NM_000548.5(TSC2):c.5234_5238del (p.Arg1745fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 28, 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:: RCV003482234.2

Allele description [Variation Report for NM_000548.5(TSC2):c.5234_5238del (p.Arg1745fs)]

NM_000548.5(TSC2):c.5234_5238del (p.Arg1745fs)

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.5234_5238del (p.Arg1745fs)

HGVS:

NC_000016.10:g.2088300_2088304del
NG_005895.1:g.43995_43999del
NG_008617.1:g.54918_54922del
NM_000548.3:c.5234_5238del
NM_000548.5:c.5234_5238delMANE SELECT
NM_001077183.3:c.5033_5037del
NM_001114382.3:c.5165_5169del
NM_001318827.2:c.4925_4929del
NM_001318829.2:c.4889_4893del
NM_001318831.2:c.4502_4506del
NM_001318832.2:c.5066_5070del
NM_001363528.2:c.5036_5040del
NM_001370404.1:c.5102_5106del
NM_001370405.1:c.5093_5097del
NM_021055.3:c.5105_5109del
NP_000539.2:p.Arg1745fs
NP_001070651.1:p.Arg1678fs
NP_001107854.1:p.Arg1722fs
NP_001305756.1:p.Arg1642fs
NP_001305758.1:p.Arg1630fs
NP_001305760.1:p.Arg1501fs
NP_001305761.1:p.Arg1689fs
NP_001350457.1:p.Arg1679fs
NP_001357333.1:p.Arg1701fs
NP_001357334.1:p.Arg1698fs
NP_066399.2:p.Arg1702fs
LRG_487t1:c.5234_5238del
LRG_487:g.43995_43999del
NC_000016.9:g.2138301_2138305del
p.(=)
p.(Arg1745Hisfs*28)

Protein change:

R1501fs

Links:

Tuberous sclerosis database (TSC2): TSC2_00947; dbSNP: rs137854002

NCBI 1000 Genomes Browser:

rs137854002

Molecular consequence:

NM_000548.5:c.5234_5238del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001077183.3:c.5033_5037del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001114382.3:c.5165_5169del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318827.2:c.4925_4929del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318829.2:c.4889_4893del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318831.2:c.4502_4506del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318832.2:c.5066_5070del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001363528.2:c.5036_5040del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370404.1:c.5102_5106del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370405.1:c.5093_5097del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_021055.3:c.5105_5109del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004229365	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Jun 28, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004229365

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Jun 28, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Athena Diagnostics, SCV004229365.1

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

Description

This variant is expected to result in the loss of a functional protein. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org).

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

Last Updated: Jun 2, 2024

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