NM_000548.5(TSC2):c.4597CTC[1] (p.Leu1534del) AND Tuberous sclerosis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 21, 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:: RCV003628507.2

Allele description [Variation Report for NM_000548.5(TSC2):c.4597CTC[1] (p.Leu1534del)]

NM_000548.5(TSC2):c.4597CTC[1] (p.Leu1534del)

Gene:

TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.4597CTC[1] (p.Leu1534del)

HGVS:

NC_000016.10:g.2085257CTC[1]
NG_005895.1:g.40952CTC[1]
NM_000548.5:c.4597CTC[1]MANE SELECT
NM_001077183.3:c.4396CTC[1]
NM_001114382.3:c.4528CTC[1]
NM_001318827.2:c.4288CTC[1]
NM_001318829.2:c.4252CTC[1]
NM_001318831.2:c.3865CTC[1]
NM_001318832.2:c.4429CTC[1]
NM_001363528.2:c.4399CTC[1]
NM_001370404.1:c.4465CTC[1]
NM_001370405.1:c.4468CTC[1]
NM_001406663.1:c.4594CTC[1]
NM_001406664.1:c.4525CTC[1]
NM_001406665.1:c.4519CTC[1]
NM_001406667.1:c.4489CTC[1]
NM_001406668.1:c.4486CTC[1]
NM_001406670.1:c.4417CTC[1]
NM_001406671.1:c.4387CTC[1]
NM_001406673.1:c.4384CTC[1]
NM_001406675.1:c.4381CTC[1]
NM_001406676.1:c.4378CTC[1]
NM_001406677.1:c.4339CTC[1]
NM_001406678.1:c.4285CTC[1]
NM_001406679.1:c.4249CTC[1]
NM_001406680.1:c.3997CTC[1]
NM_001406681.1:c.3937CTC[1]
NM_001406682.1:c.3928CTC[1]
NM_001406683.1:c.3928CTC[1]
NM_001406684.1:c.3925CTC[1]
NM_001406685.1:c.3799CTC[1]
NM_001406686.1:c.3799CTC[1]
NM_001406687.1:c.3796CTC[1]
NM_001406688.1:c.3796CTC[1]
NM_001406689.1:c.3184CTC[1]
NM_001406690.1:c.3124CTC[1]
NM_001406691.1:c.3121CTC[1]
NM_001406692.1:c.3055CTC[1]
NM_001406693.1:c.3055CTC[1]
NM_001406694.1:c.3055CTC[1]
NM_001406695.1:c.3052CTC[1]
NM_001406696.1:c.3052CTC[1]
NM_001406697.1:c.3052CTC[1]
NM_001406698.1:c.2794CTC[1]
NM_021055.3:c.4468CTC[1]
NP_000539.2:p.Leu1534del
NP_000539.2:p.Leu1534del
NP_001070651.1:p.Leu1467del
NP_001107854.1:p.Leu1511del
NP_001305756.1:p.Leu1431del
NP_001305758.1:p.Leu1419del
NP_001305760.1:p.Leu1290del
NP_001305761.1:p.Leu1478del
NP_001350457.1:p.Leu1468del
NP_001357333.1:p.Leu1490del
NP_001357334.1:p.Leu1491del
NP_001393592.1:p.Leu1533del
NP_001393593.1:p.Leu1510del
NP_001393594.1:p.Leu1508del
NP_001393596.1:p.Leu1498del
NP_001393597.1:p.Leu1497del
NP_001393599.1:p.Leu1474del
NP_001393600.1:p.Leu1464del
NP_001393602.1:p.Leu1463del
NP_001393604.1:p.Leu1462del
NP_001393605.1:p.Leu1461del
NP_001393606.1:p.Leu1448del
NP_001393607.1:p.Leu1430del
NP_001393608.1:p.Leu1418del
NP_001393609.1:p.Leu1334del
NP_001393610.1:p.Leu1314del
NP_001393611.1:p.Leu1311del
NP_001393612.1:p.Leu1311del
NP_001393613.1:p.Leu1310del
NP_001393614.1:p.Leu1268del
NP_001393615.1:p.Leu1268del
NP_001393616.1:p.Leu1267del
NP_001393617.1:p.Leu1267del
NP_001393618.1:p.Leu1063del
NP_001393619.1:p.Leu1043del
NP_001393620.1:p.Leu1042del
NP_001393621.1:p.Leu1020del
NP_001393622.1:p.Leu1020del
NP_001393623.1:p.Leu1020del
NP_001393624.1:p.Leu1019del
NP_001393625.1:p.Leu1019del
NP_001393626.1:p.Leu1019del
NP_001393627.1:p.Leu933del
NP_066399.2:p.Leu1491del
LRG_487t1:c.4597_4599CTC[1]
LRG_487:g.40952CTC[1]
LRG_487p1:p.Leu1534del
NC_000016.9:g.2135258CTC[1]
NC_000016.9:g.2135258_2135260del
NM_000548.3:c.4597_4599CTC[1]
NR_176225.1:n.4549CTC[1]
NR_176226.1:n.4797CTC[1]
NR_176227.1:n.4725CTC[1]
NR_176228.1:n.4546CTC[1]
NR_176229.1:n.4506CTC[1]

Protein change:

L1019del

Molecular consequence:

NM_000548.5:c.4597CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001077183.3:c.4396CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001114382.3:c.4528CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318827.2:c.4288CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318829.2:c.4252CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318831.2:c.3865CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318832.2:c.4429CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001363528.2:c.4399CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370404.1:c.4465CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370405.1:c.4468CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406663.1:c.4594CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406664.1:c.4525CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406665.1:c.4519CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406667.1:c.4489CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406668.1:c.4486CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406670.1:c.4417CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406671.1:c.4387CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406673.1:c.4384CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406675.1:c.4381CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406676.1:c.4378CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406677.1:c.4339CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406678.1:c.4285CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406679.1:c.4249CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406680.1:c.3997CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406681.1:c.3937CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406682.1:c.3928CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406683.1:c.3928CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406684.1:c.3925CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406685.1:c.3799CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406686.1:c.3799CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406687.1:c.3796CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406688.1:c.3796CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406689.1:c.3184CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406690.1:c.3124CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406691.1:c.3121CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406692.1:c.3055CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406693.1:c.3055CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406694.1:c.3055CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406695.1:c.3052CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406696.1:c.3052CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406697.1:c.3052CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406698.1:c.2794CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_021055.3:c.4468CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_176225.1:n.4549CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176226.1:n.4797CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176227.1:n.4725CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176228.1:n.4546CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176229.1:n.4506CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004447011	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 21, 2023)	germline	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

SCV004447011

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 21, 2023)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004447011.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with TSC2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.4600_4602del, results in the deletion of 1 amino acid(s) of the TSC2 protein (p.Leu1534del), but otherwise preserves the integrity of the reading frame.

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

Last Updated: Sep 29, 2024

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