NM_000368.5(TSC1):c.2620A>C (p.Thr874Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 27, 2021
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:: RCV000562317.5

Allele description [Variation Report for NM_000368.5(TSC1):c.2620A>C (p.Thr874Pro)]

NM_000368.5(TSC1):c.2620A>C (p.Thr874Pro)

Gene:

TSC1:TSC complex subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_000368.5(TSC1):c.2620A>C (p.Thr874Pro)

HGVS:

NC_000009.12:g.132900720T>G
NG_012386.1:g.48914A>C
NM_000368.5:c.2620A>CMANE SELECT
NM_001162426.2:c.2617A>C
NM_001162427.2:c.2467A>C
NM_001362177.2:c.2257A>C
NP_000359.1:p.Thr874Pro
NP_000359.1:p.Thr874Pro
NP_001155898.1:p.Thr873Pro
NP_001155899.1:p.Thr823Pro
NP_001349106.1:p.Thr753Pro
LRG_486t1:c.2620A>C
LRG_486:g.48914A>C
LRG_486p1:p.Thr874Pro
NC_000009.11:g.135776107T>G
NM_000368.4:c.2620A>C

Protein change:

T753P

Links:

dbSNP: rs1554814368

NCBI 1000 Genomes Browser:

rs1554814368

Molecular consequence:

NM_000368.5:c.2620A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001162426.2:c.2617A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001162427.2:c.2467A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001362177.2:c.2257A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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6720468P15Rik RIKEN cDNA 6720468P15 gene [Mus musculus]
6720468P15Rik RIKEN cDNA 6720468P15 gene [Mus musculus]
Gene ID:78073

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000675450	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 25, 2016)	germline	clinical testing	Citation Link,
SCV002528874	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Jun 27, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000675450

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 25, 2016)

germline

clinical testing

Citation Link,

SCV002528874

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Jun 27, 2021)

germline

curation

Citation Link

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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, curation

Details of each submission

From Ambry Genetics, SCV000675450.5

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

Description

The p.T874P variant (also known as c.2620A>C), located in coding exon 18 of the TSC1 gene, results from an A to C substitution at nucleotide position 2620. The threonine at codon 874 is replaced by proline, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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 Sema4, Sema4, SCV002528874.1

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

#	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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