NM_000142.5(FGFR3):c.2413C>T (p.Arg805Trp) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 14, 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:: RCV002235308.14

Allele description [Variation Report for NM_000142.5(FGFR3):c.2413C>T (p.Arg805Trp)]

NM_000142.5(FGFR3):c.2413C>T (p.Arg805Trp)

Gene:

FGFR3:fibroblast growth factor receptor 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_000142.5(FGFR3):c.2413C>T (p.Arg805Trp)

HGVS:

NC_000004.12:g.1807254C>T
NG_012632.1:g.18943C>T
NM_000142.5:c.2413C>TMANE SELECT
NM_001163213.2:c.2419C>T
NM_001354809.2:c.2416C>T
NM_001354810.2:c.2345C>T
NM_022965.4:c.2077C>T
NP_000133.1:p.Arg805Trp
NP_000133.1:p.Arg805Trp
NP_001156685.1:p.Arg807Trp
NP_001341738.1:p.Arg806Trp
NP_001341739.1:p.Ala782Val
NP_075254.1:p.Arg693Trp
LRG_1021t1:c.2413C>T
LRG_1021:g.18943C>T
LRG_1021p1:p.Arg805Trp
NC_000004.11:g.1808981C>T
NM_000142.4:c.2413C>T
NR_148971.2:n.2839C>T

Protein change:

A782V

Links:

dbSNP: rs369758941

NCBI 1000 Genomes Browser:

rs369758941

Molecular consequence:

NM_000142.5:c.2413C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001163213.2:c.2419C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354809.2:c.2416C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354810.2:c.2345C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022965.4:c.2077C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148971.2:n.2839C>T - 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
SCV000946868	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 14, 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

SCV000946868

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 14, 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, SCV000946868.4

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 805 of the FGFR3 protein (p.Arg805Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with FGFR3-related conditions. ClinVar contains an entry for this variant (Variation ID: 651478). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on FGFR3 protein function. 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.

#	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: Nov 24, 2024

ClinVar

Relating variation to medicine