NM_000548.5(TSC2):c.5150T>C (p.Leu1717Pro) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 21, 2014
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:: RCV000190040.1

Allele description

NM_000548.5(TSC2):c.5150T>C (p.Leu1717Pro)

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.5150T>C (p.Leu1717Pro)

Other names:

p.L1717P:CTG>CCG

HGVS:

NC_000016.10:g.2088129T>C
NG_005895.1:g.43824T>C
NG_008617.1:g.55092A>G
NM_000548.5:c.5150T>CMANE SELECT
NM_001077183.2:c.4949T>C
NM_001114382.2:c.5081T>C
NM_001318827.1:c.4841T>C
NM_001318829.1:c.4805T>C
NM_001318831.1:c.4418T>C
NM_001318832.1:c.4982T>C
NM_001363528.1:c.4952T>C
NM_001370404.1:c.5018T>C
NM_001370405.1:c.5021T>C
NM_021055.2:c.5021T>C
NP_000539.2:p.Leu1717Pro
NP_001070651.1:p.Leu1650Pro
NP_001107854.1:p.Leu1694Pro
NP_001305756.1:p.Leu1614Pro
NP_001305758.1:p.Leu1602Pro
NP_001305760.1:p.Leu1473Pro
NP_001305761.1:p.Leu1661Pro
NP_001350457.1:p.Leu1651Pro
NP_001357333.1:p.Leu1673Pro
NP_001357334.1:p.Leu1674Pro
NP_066399.2:p.Leu1674Pro
LRG_487t1:c.5150T>C
LRG_487:g.43824T>C
NC_000016.9:g.2138130T>C
NM_000548.3:c.5150T>C
p.(Leu1717Pro)

Protein change:

L1473P

Links:

Tuberous sclerosis database (TSC2): TSC2_00684; dbSNP: rs45517398

NCBI 1000 Genomes Browser:

rs45517398

Molecular consequence:

NM_000548.5:c.5150T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.2:c.4949T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.2:c.5081T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.1:c.4841T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.1:c.4805T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.1:c.4418T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.1:c.4982T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.1:c.4952T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5018T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5021T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.2:c.5021T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000243714	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 21, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000243714

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 21, 2014)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000243714.10

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

Description

p.Leu1717Pro (CTG>CCG): c.5150 T>C in exon 40 of the TSC2 gene (NM_000548.3). The Leu1717Pro missense mutation in the TSC2 gene has been reported previously as a de novo mutation in a patient with cardiac rhabdomyomas, hypopigmentation of the skin, subependymal nodules, and seizures beginning at 1 year of age (Chen et al., 2005). This mutation is reported in the TSC2 LOVD database in three additional patients. It was not observed in approximately 6,400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Leu1717Pro is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is highly conserved across species and many other missense mutations associated with TSC2-related disorders have been reported in this region of the protein. The variant is found in INFANT-EPI panel(s).

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

Last Updated: Feb 27, 2021

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