NM_000548.5(TSC2):c.5209C>T (p.Pro1737Ser) AND Tuberous sclerosis 2

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 3, 2024
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:: RCV000226974.13

Allele description [Variation Report for NM_000548.5(TSC2):c.5209C>T (p.Pro1737Ser)]

NM_000548.5(TSC2):c.5209C>T (p.Pro1737Ser)

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.5209C>T (p.Pro1737Ser)

HGVS:

NC_000016.10:g.2088275C>T
NG_005895.1:g.43970C>T
NG_008617.1:g.54946G>A
NM_000548.5:c.5209C>TMANE SELECT
NM_001077183.3:c.5008C>T
NM_001114382.3:c.5140C>T
NM_001318827.2:c.4900C>T
NM_001318829.2:c.4864C>T
NM_001318831.2:c.4477C>T
NM_001318832.2:c.5041C>T
NM_001363528.2:c.5011C>T
NM_001370404.1:c.5077C>T
NM_001370405.1:c.5068C>T
NM_021055.3:c.5080C>T
NP_000539.2:p.Pro1737Ser
NP_001070651.1:p.Pro1670Ser
NP_001107854.1:p.Pro1714Ser
NP_001305756.1:p.Pro1634Ser
NP_001305758.1:p.Pro1622Ser
NP_001305760.1:p.Pro1493Ser
NP_001305761.1:p.Pro1681Ser
NP_001350457.1:p.Pro1671Ser
NP_001357333.1:p.Pro1693Ser
NP_001357334.1:p.Pro1690Ser
NP_066399.2:p.Pro1694Ser
LRG_487t1:c.5209C>T
LRG_487:g.43970C>T
NC_000016.9:g.2138276C>T
NM_000548.3:c.5209C>T

Protein change:

P1493S

Links:

dbSNP: rs780112037

NCBI 1000 Genomes Browser:

rs780112037

Molecular consequence:

NM_000548.5:c.5209C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.5008C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5140C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.4900C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.4864C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4477C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5041C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.5011C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5077C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5068C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5080C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Azoarcus taiwanensis strain:NSC3
Azoarcus taiwanensis strain:NSC3
Azoarcus taiwanensis strain:NSC3 Genome sequencing and assembly

BioProject
Chain A, PROTEIN NDRG2
Chain A, PROTEIN NDRG2
gi|319443314|pdb|2XMR|A

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000285451	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 3, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002040260	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 7, 2021)	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

SCV000285451

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 3, 2024)

germline

clinical testing

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

SCV002040260

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Nov 7, 2021)

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000285451.9

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

#	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

From Genome-Nilou Lab, SCV002040260.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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