ClinVar Genomic variation as it relates to human health
NM_000142.5(FGFR3):c.1138G>C (p.Gly380Arg)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000142.5(FGFR3):c.1138G>C (p.Gly380Arg)
Variation ID: 16328 Accession: VCV000016328.56
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4p16.3 4: 1804392 (GRCh38) [ NCBI UCSC ] 4: 1806119 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Oct 8, 2024 May 20, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000142.5:c.1138G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000133.1:p.Gly380Arg missense NM_001163213.2:c.1144G>C NP_001156685.1:p.Gly382Arg missense NM_001354809.2:c.1138G>C NP_001341738.1:p.Gly380Arg missense NM_001354810.2:c.1138G>C NP_001341739.1:p.Gly380Arg missense NM_022965.4:c.931-432G>C intron variant NR_148971.2:n.1564G>C non-coding transcript variant NC_000004.12:g.1804392G>C NC_000004.11:g.1806119G>C NG_012632.1:g.16081G>C LRG_1021:g.16081G>C LRG_1021t1:c.1138G>C LRG_1021p1:p.Gly380Arg P22607:p.Gly380Arg - Protein change
- G380R, G382R
- Other names
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FGFR3, GLY380ARG, 1138G-C
- Canonical SPDI
- NC_000004.12:1804391:G:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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FGFR3 | No evidence available | No evidence available |
GRCh38 GRCh37 |
984 | 1134 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Sep 1, 2022 | RCV000017725.42 | |
Pathogenic (2) |
criteria provided, single submitter
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May 28, 2019 | RCV000987394.11 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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May 20, 2024 | RCV000727147.28 | |
FGFR3-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Aug 23, 2024 | RCV004532375.2 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Apr 28, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV002049731.1
First in ClinVar: Jan 08, 2022 Last updated: Jan 08, 2022 |
Comment:
The FGFR3 c.1138G>C; p.Gly380Arg variant (rs28931614) is a common pathogenic variant observed in individuals affected with achondroplasia (Rousseau 1994, Xue 2014). This variant is absent … (more)
The FGFR3 c.1138G>C; p.Gly380Arg variant (rs28931614) is a common pathogenic variant observed in individuals affected with achondroplasia (Rousseau 1994, Xue 2014). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. Functional characterization of the variant protein suggests it causes ligand-independent phosphorylation of ERK and reduced proliferation of chondrocytes (Krejci 2008). A mouse model expressing the p.Gly380Arg variant recapitulates skeletal alterations observed in human achondroplasia patients (Lee 2017). Additionally, another variant at this codon causing the same amino substitution (c.1138G>A; p.Gly380Arg) is commonly reported in individuals with achondroplasia and is considered pathogenic (Rousseau 1994, Xue 2014). Based on available information, the c.1138G>C; p.Gly380Arg variant is considered to be pathogenic. References: Krejci P et al. Analysis of STAT1 activation by six FGFR3 mutants associated with skeletal dysplasia undermines dominant role of STAT1 in FGFR3 signaling in cartilage. PLoS One. 2008;3(12):e3961.. PMID: 19088846. Lee YC et al. Knock-in human FGFR3 achondroplasia mutation as a mouse model for human skeletal dysplasia. Sci Rep. 2017 Feb 23;7:43220. PMID: 28230213. Rousseau F et al. Mutations in the gene encoding fibroblast growth factor receptor-3 in achondroplasia. Nature. 1994 Sep 15;371(6494):252-4. PMID: 8078586. Xue Y et al. FGFR3 mutation frequency in 324 cases from the International Skeletal Dysplasia Registry. Mol Genet Genomic Med. 2014 Nov;2(6):497-503. PMID: 25614871. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Achondroplasia
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004171370.1
First in ClinVar: Dec 02, 2023 Last updated: Dec 02, 2023 |
Clinical Features:
Neonatal short-limb short stature (present)
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Pathogenic
(Apr 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002023073.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Dec 09, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000762848.5
First in ClinVar: May 28, 2018 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 380 of the FGFR3 protein (p.Gly380Arg). … (more)
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 380 of the FGFR3 protein (p.Gly380Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with achondroplasia (PMID: 8723101, 21739570, 22045636, 22339077, 25614871, 25691418). ClinVar contains an entry for this variant (Variation ID: 16328). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is expected to disrupt FGFR3 function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Feb 21, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000706143.2
First in ClinVar: Jul 25, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Pathogenic
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Hypochondroplasia
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001136682.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Pathogenic
(Sep 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Achondroplasia
Affected status: yes
Allele origin:
germline
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3billion
Accession: SCV002573180.1
First in ClinVar: Sep 17, 2022 Last updated: Sep 17, 2022 |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of … (more)
The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.71; 3Cnet: 0.92). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000016328). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 25614871). A different missense change at the same codon (p.Gly380Lys) has been reported to be associated with FGFR3-related disorder (PMID: 17256796). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Short stature (present) , Macrocephaly (present) , Limb undergrowth (present)
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Pathogenic
(May 20, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001871012.3
First in ClinVar: Sep 19, 2021 Last updated: Sep 16, 2024 |
Comment:
More than 99% of cases of achondroplasia are caused by this variant and another point mutation (c.1138 G>A) resulting in arginine-for-glycine substitutions in amino acid … (more)
More than 99% of cases of achondroplasia are caused by this variant and another point mutation (c.1138 G>A) resulting in arginine-for-glycine substitutions in amino acid 380 of the gene (Foldynova-Trantirkova et al., 2012; Shiang et al., 1994); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 33370388, 31566912, 33368972, 28679403, 8078586, 8723101, 33511985, 29542187, 7913883, 25614871, 17683901, 25691418, 9857065, 23056398, 19088846, 28230213, 29593476, 21739570, 22339077, 22325359, 28181399, 30160829, 30138938, 34672771, 22045636, 36352425, 36923788) (less)
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Pathogenic
(Sep 15, 1994)
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no assertion criteria provided
Method: literature only
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ACHONDROPLASIA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000038003.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 09, 2024 |
Comment on evidence:
Rousseau et al. (1994) found the gly380-to-arg mutation in all 23 cases of achondroplasia (ACH; 100800) studied (17 sporadic and 6 familial). Twenty-two of the … (more)
Rousseau et al. (1994) found the gly380-to-arg mutation in all 23 cases of achondroplasia (ACH; 100800) studied (17 sporadic and 6 familial). Twenty-two of the 23 probands had the G-to-A transition (134934.0001); only 1 had the G-to-C transversion. (less)
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Pathogenic
(Aug 23, 2024)
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no assertion criteria provided
Method: clinical testing
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FGFR3-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004735024.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The FGFR3 c.1138G>C variant is predicted to result in the amino acid substitution p.Gly380Arg. The p.Gly380Arg variant has been well documented to be causative for … (more)
The FGFR3 c.1138G>C variant is predicted to result in the amino acid substitution p.Gly380Arg. The p.Gly380Arg variant has been well documented to be causative for autosomal dominant achondroplasia (see examples: Shiang et al. 1994. PubMed ID: 7913883; Bellus et al. 1995. PubMed ID: 7847369). This variant has not been reported in gnomAD, indicating this variant is rare. This variant is interpreted as pathogenic. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Hypochondroplasia
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV002318922.2
First in ClinVar: Apr 02, 2022 Last updated: Oct 01, 2022 |
Comment:
Common pathogenic variant in achondroplasia
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Hypochondroplasia. | Adam MP | - | 2020 | PMID: 20301650 |
Association of achondroplasia with sagittal synostosis and scaphocephaly in two patients, an underestimated condition? | Accogli A | American journal of medical genetics. Part A | 2015 | PMID: 25691418 |
FGFR3 mutation frequency in 324 cases from the International Skeletal Dysplasia Registry. | Xue Y | Molecular genetics & genomic medicine | 2014 | PMID: 25614871 |
Rapid detection of G1138A and G1138C mutations of the FGFR3 gene in patients with achondroplasia using high-resolution melting analysis. | He X | Genetic testing and molecular biomarkers | 2012 | PMID: 22339077 |
Sixteen years and counting: the current understanding of fibroblast growth factor receptor 3 (FGFR3) signaling in skeletal dysplasias. | Foldynova-Trantirkova S | Human mutation | 2012 | PMID: 22045636 |
Achondroplasia with synostosis of multiple sutures. | Georgoulis G | American journal of medical genetics. Part A | 2011 | PMID: 21739570 |
Clinical hypochondroplasia in a family caused by a heterozygous double mutation in FGFR3 encoding GLY380LYS. | Santos HG | American journal of medical genetics. Part A | 2007 | PMID: 17256796 |
Common mutations in the fibroblast growth factor receptor 3 (FGFR 3) gene account for achondroplasia, hypochondroplasia, and thanatophoric dwarfism. | Bonaventure J | American journal of medical genetics | 1996 | PMID: 8723101 |
Mutations in the gene encoding fibroblast growth factor receptor-3 in achondroplasia. | Rousseau F | Nature | 1994 | PMID: 8078586 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=FGFR3 | - | - | - | - |
Text-mined citations for rs28931614 ...
HelpRecord last updated Nov 19, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.