NM_000245.4(MET):c.2312_2315del (p.Ser771fs) AND Renal cell carcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 2, 2021
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:: RCV001914802.4

Allele description [Variation Report for NM_000245.4(MET):c.2312_2315del (p.Ser771fs)]

NM_000245.4(MET):c.2312_2315del (p.Ser771fs)

Gene:

MET:MET proto-oncogene, receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000245.4(MET):c.2312_2315del (p.Ser771fs)

HGVS:

NC_000007.14:g.116759438_116759441del
NG_008996.1:g.92034_92037del
NM_000245.4:c.2312_2315delMANE SELECT
NM_001127500.3:c.2366_2369del
NM_001324401.3:c.2312_2315del
NM_001324402.2:c.1022_1025del
NP_000236.2:p.Ser771fs
NP_001120972.1:p.Ser789fs
NP_001311330.1:p.Ser771fs
NP_001311331.1:p.Ser341fs
LRG_662:g.92034_92037del
NC_000007.13:g.116399492_116399495del

Protein change:

S341fs

Links:

dbSNP: rs2116938318

NCBI 1000 Genomes Browser:

rs2116938318

Molecular consequence:

NM_000245.4:c.2312_2315del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127500.3:c.2366_2369del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001324401.3:c.2312_2315del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001324402.2:c.1022_1025del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Renal cell carcinoma (RCCP1)
Identifiers:: MONDO: MONDO:0005086; MeSH: D002292; MedGen: C0007134; Human Phenotype Ontology: HP:0005584

Recent activity

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interleukin 8 (74079)
PMC
endoglucanase 24 [Jatropha curcas]
endoglucanase 24 [Jatropha curcas]
gi|802708133|ref|XP_012084447.1|

Protein
PREDICTED: Homo sapiens leucine zipper protein 2 (LUZP2), transcript variant X3,...
PREDICTED: Homo sapiens leucine zipper protein 2 (LUZP2), transcript variant X3, mRNA
gi|1370459246|ref|XM_017017649.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002147190	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 2, 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

SCV002147190

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 2, 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	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, SCV002147190.3

#	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. This variant has not been reported in the literature in individuals affected with MET-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ser789Thrfs*6) in the MET gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in MET cause disease.

#	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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