NM_000141.5(FGFR2):c.1019A>G (p.Tyr340Cys) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Nov 25, 2022
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:: RCV000523700.9

Allele description [Variation Report for NM_000141.5(FGFR2):c.1019A>G (p.Tyr340Cys)]

NM_000141.5(FGFR2):c.1019A>G (p.Tyr340Cys)

Gene:

FGFR2:fibroblast growth factor receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q26.13

Genomic location:

Preferred name:

NM_000141.5(FGFR2):c.1019A>G (p.Tyr340Cys)

HGVS:

NC_000010.11:g.121517384T>C
NG_012449.2:g.86075A>G
NM_000141.5:c.1019A>GMANE SELECT
NM_001144913.1:c.1087+1298A>G
NM_001144914.1:c.749-2065A>G
NM_001144915.2:c.752A>G
NM_001144916.2:c.674A>G
NM_001144917.2:c.939+2595A>G
NM_001144918.2:c.674A>G
NM_001144919.2:c.820+1298A>G
NM_001320654.2:c.335A>G
NM_001320658.2:c.1019A>G
NM_022970.4:c.1087+1298A>G
NM_023029.2:c.752A>G
NP_000132.3:p.Tyr340Cys
NP_000132.3:p.Tyr340Cys
NP_001138387.1:p.Tyr251Cys
NP_001138388.1:p.Tyr225Cys
NP_001138390.1:p.Tyr225Cys
NP_001307583.1:p.Tyr112Cys
NP_001307587.1:p.Tyr340Cys
NP_075418.1:p.Tyr251Cys
LRG_994t1:c.1019A>G
LRG_994:g.86075A>G
LRG_994p1:p.Tyr340Cys
NC_000010.10:g.123276898T>C
NM_000141.4:c.1019A>G
NR_073009.2:n.1455A>G

Protein change:

Y112C

Links:

dbSNP: rs1554928884

NCBI 1000 Genomes Browser:

rs1554928884

Molecular consequence:

NM_001144913.1:c.1087+1298A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001144914.1:c.749-2065A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001144917.2:c.939+2595A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001144919.2:c.820+1298A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_022970.4:c.1087+1298A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000141.5:c.1019A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001144915.2:c.752A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001144916.2:c.674A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001144918.2:c.674A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001320654.2:c.335A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001320658.2:c.1019A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_023029.2:c.752A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_073009.2:n.1455A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000617522	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 25, 2022)	germline	clinical testing	Citation Link,
SCV001954673	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001968524	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV003822014	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 25, 2022)	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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 GeneDx, SCV000617522.4

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

Description

Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23754559, 10394936, 16418739, 18671283, 22987770, 24863959, 26858415, 25271085, 15305355, 27683237, 34366428)

#	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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001954673.1

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

#	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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001968524.1

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

#	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

From Revvity Omics, Revvity, SCV003822014.2

#	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

Last Updated: Mar 16, 2024

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