4-1801844-C-G
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Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_000142.5(FGFR3):c.749C>G(p.Pro250Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,606,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
FGFR3
NM_000142.5 missense
NM_000142.5 missense
Scores
11
3
5
Clinical Significance
Conservation
PhyloP100: 5.85
Genes affected
FGFR3 (HGNC:3690): (fibroblast growth factor receptor 3) This gene encodes a member of the fibroblast growth factor receptor (FGFR) family, with its amino acid sequence being highly conserved between members and among divergent species. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein would consist of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member binds acidic and basic fibroblast growth hormone and plays a role in bone development and maintenance. Mutations in this gene lead to craniosynostosis and multiple types of skeletal dysplasia. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.989
PP5
Variant 4-1801844-C-G is Pathogenic according to our data. Variant chr4-1801844-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 16340.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-1801844-C-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FGFR3 | NM_000142.5 | c.749C>G | p.Pro250Arg | missense_variant | 7/18 | ENST00000440486.8 | NP_000133.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FGFR3 | ENST00000440486.8 | c.749C>G | p.Pro250Arg | missense_variant | 7/18 | 5 | NM_000142.5 | ENSP00000414914 | P4 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000418 AC: 1AN: 238970Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131106
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GnomAD4 exome AF: 0.0000117 AC: 17AN: 1454808Hom.: 0 Cov.: 39 AF XY: 0.0000111 AC XY: 8AN XY: 722916
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:42Other:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Muenke syndrome Pathogenic:19
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) | Apr 01, 2023 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Mar 05, 2021 | This variant was identified as de novo (maternity and paternity confirmed). - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Feb 22, 2021 | The FGFR3 c.749C>G variant is a single nucleotide change in the FGFR3 gene that changes the amino acid proline at position 250 in the protein to arginine. This variant has been previously reported in several unrelated patients with Muenke syndrome (PMID: 9042914, 26740388, 20301628) (PS4_moderate). Functional characterization demonstrates that this missense change enhances ligand-binding in vitro compared to wild-type and affects endochondral ossification (PMID: 14613973, 22016144) (PS3). The variant was detected de novo in a patient with no family history of the disease (PS2). This variant has been reported in dbSNP (rs4647924) and is rare in population databases (2/270,300 in gnomAD, 0 homozygotes) (PM2). It is a non-conservative amino acid substitution and is predicted by multiple in silico tools to be deleterious to protein function (PP3). - |
| Pathogenic, criteria provided, single submitter | clinical testing | Suma Genomics | - | - - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2009 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | Dec 20, 2021 | PS4, PM2, PP3, PP5 - |
| Pathogenic, criteria provided, single submitter | research | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Oct 04, 2024 | PS1, PS3, PM2 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego | Apr 24, 2018 | This variant is a well-established cause of Muenke syndrome (PMID: 9042914, 26740388, 20301628). Functional characterization demonstrates that this missense change enhances ligand-binding in vitro compared to wild-type and affects endochondral ossification (PMID: 14613973, 22016144). This variant is present as a heterozygous change in the gnomAD population database at a frequency of 0.001% (2/267,378) and is thus presumed to be rare. It is a non-conservative amino acid substitution and is predicted by multiple in silico tools to be deleterious to protein function. Based on the combined evidence, the c.749C>G (p.Pro250Arg) variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Feb 28, 2022 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | May 06, 2020 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Mar 31, 2022 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with autosomal dominant skeletal dysplasias (OMIM). Additionally, autosomal recessive and dominant CATSHL syndrome (MIM#610474), is suspected to be due to variants with a loss of function, and dominant negative mechanism, respectively (PMID: 25614871, PMID: 24864036). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance. Individuals with Muenke syndrome have been shown to inherit pathogenic variants from an asymptomatic parent (PMID: 26740388, PMID: 18000976). (I) 0115 - Variants in this gene are known to have variable expressivity. There is a wide range of clinical symptoms with variable expressivity in LADD and Muenke syndrome patients, even within the same family (PMID: 26740388, PMID: 16501574). (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to arginine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (2 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2, v3) (2 heterozygotes, 0 homozygotes). (I) 0504 - Same amino acid change has been observed in placental mammals. (SB) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is very well established as pathogenic, and has been reported in many individuals with Muenke syndrome with variable expressivity. Additionally, it has been observed less commonly in individuals with Saethre-Chotzen or craniosynostosis syndrome, and can be inherited from an asymptomatic parent (ClinVar, PMID: 26740388). (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Oct 20, 2016 | - - |
| Likely pathogenic, criteria provided, single submitter | research | Cavalleri Lab, Royal College of Surgeons in Ireland | Dec 11, 2019 | ACMG evidence PS3, PP2, PP3 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Aug 26, 2022 | ACMG classification criteria: PS3 supporting, PS4 strong, PM2 supporting, PM6 strong, PP3 supporting - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Dec 28, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Sep 05, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital | Feb 04, 2022 | Muenke syndrome (MIM #602849) is diagnosed based on the presence of the recurrent p.Pro250Arg variant (PMID: 8841188). - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Medical Genetics, Oslo University Hospital | - | - - |
not provided Pathogenic:10
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 27, 2019 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 27, 2020 | Reported in multiple individuals with features overlapping other craniosynostosis syndromes, including Pfeiffer syndrome, Crouzon syndrome, and Saethre-Chotzen syndrome (Bellus et al., 1996; Muenke et al., 1997; Mulliken et al., 1999; Kruszka et al., 2016); however, some of the clinical features of individuals with the above syndromes may be rare in patients with this variant (Muenke et al., 1997); Reported in some individuals with radiographic abnormalities of hands and feet but without craniosynostosis, having normal head size or macrocephaly (Muenke et al., 1997; Kruszka et al., 2016a); Published functional studies demonstrate a damaging effect including disruption of endochondral and perichondrial ossification of the cranial base in mice (Laurita et al., 2011; Yasuda et al., 2012); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); 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: 11746040, 22622662, 24127277, 28551036, 31837199, 14613973, 26740388, 11424131, 12884424, 23325524, 19449410, 21204234, 22016144, 24705944, 15915095, 21233754, 21403567, 22446440, 23851839, 20592905, 24168007, 11197897, 24728327, 12087222, 20707699, 11428324, 8841188, 10541159, 27683237, 27568649, 26028288, 9279764, 9600744, 17103449, 17036334, 31111620, 31130284, 9042914, 20301588, 32238909, 31564432, 31019026, 32369273, 32382396, 9107244, 18000976, 32510873, 33502061) - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | FGFR3: PP1:Strong, PM2, PM5, PS3:Moderate, PP3, PP4, PS4:Supporting - |
| Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics Laboratory, Skane University Hospital Lund | Jul 13, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 06, 2023 | This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 250 of the FGFR3 protein (p.Pro250Arg). This variant is present in population databases (rs4647924, gnomAD 0.003%). This missense change has been observed in individual(s) with Muenke syndrome, but has also been identified in individuals with features of Saethre-Chotzen syndrome or other craniosynostosis syndromes (PMID: 9042914, 10094188, 10861678, 15915095, 26740388). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 16340). 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. Experimental studies have shown that this missense change affects FGFR3 function (PMID: 14613973). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 20, 2018 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Nov 30, 2019 | - - |
Achondroplasia Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 31, 2018 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. The p.R250R pathogenic variant is the most common pathogenic variant found in MNKS patients with variable expressivity [PMID 9107244, 9279764] - |
| Pathogenic, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 17, 2024 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 22, 2024 | Variant summary: FGFR3 c.749C>G (p.Pro250Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.2e-06 in 238970 control chromosomes. c.749C>G has been reported in the literature in multiple individuals affected with Muenke syndrome (example, Paumard-Hernandez_2014). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in enhancement in ligand binding in vitro (Ibrahimi_2004). The following publications have been ascertained in the context of this evaluation (PMID: 14613973, 25271085). ClinVar contains an entry for this variant (Variation ID: 16340). Based on the evidence outlined above, the variant was classified as pathogenic. - |
FGFR3-related disorder Pathogenic:2
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 03, 2024 | The FGFR3 c.749C>G variant is predicted to result in the amino acid substitution p.Pro250Arg. This variant has been documented as one of the most common variants associated with syndromic craniosynostosis, and in particular with autosomal dominant Muenke syndrome (Muenke et al. 1997. PubMed ID: 9042914; Mulliken et al. 1999. PubMed ID: 10541159; Roscioli et al. 2013. PubMed ID: 24127277; Kruszka et al. 2016. PubMed ID: 26740388). Of note, this variant has been reported in one patient without craniosynostosis but with hearing loss and developmental delay (Patient 15, Table 1, Kruszka et al. 2016. PubMed ID: 26740388). This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Mar 26, 2024 | PS2_Very Strong, PS3, PM1, PM5_Supporting - |
FGFR3-related chondrodysplasia Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | - | - - |
Inborn genetic diseases Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.749C>G (p.P250R) alteration is located in exon 7 (coding exon 6) of the FGFR3 gene. This alteration results from a C to G substitution at nucleotide position 749, causing the proline (P) at amino acid position 250 to be replaced by an arginine (R)._x000D_ _x000D_ Based on the available evidence, the FGFR3 c.749C>G (p.P250R) alteration is classified as pathogenic for Muenke syndrome. Based on data from gnomAD, the G allele has an overall frequency of 0.001% (2/270300) total alleles studied. The highest observed frequency was 0.003% (1/34950) of Latino alleles. The FGFR3 c.749C>G (p.P250R) alteration is a well-established disease-causing alteration of Muenke syndrome and the only reported pathogenic mutation in patients with Muenke syndrome (Bellus, 1996; Kruszka, 2016). This amino acid position is well conserved in available vertebrate species. Functional analysis of mouse models of Muenke syndrome harboring the mouse equivalent of the p.P250R alteration (p.P244R in mice) show that the alteration disrupts endochondral and perichondrial ossification in the cranial base (Laurita, 2011) as well as the temporomandibular joint development by reducing hedgehog signaling and endochondral ossification (Laurita, 2011; Yasuda, 2012). Surface plasmon resonance analysis and X-ray crystallography demonstrated enhanced binding of the mutant structure compared to wildtype (Ibrahimi, 2004). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. - |
Crouzon syndrome;C0036572:Seizure;C0266294:Unilateral renal agenesis;C1306710:Facial asymmetry;C1856266:Coronal craniosynostosis;C3806604:Infantile axial hypotonia;C4316903:Generalized non-motor (absence) seizure Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Achondroplasia;C0005684:Malignant tumor of urinary bladder;C0265269:Levy-Hollister syndrome;C0334082:Epidermal nevus;C0346629:Colorectal cancer;C0410529:Hypochondroplasia;C1300257:Thanatophoric dysplasia, type 2;C1336708:Germ cell tumor of testis;C1864436:Muenke syndrome;C1864852:Camptodactyly-tall stature-scoliosis-hearing loss syndrome;C1868678:Thanatophoric dysplasia type 1;C2674173:Severe achondroplasia-developmental delay-acanthosis nigricans syndrome;C2677099:Crouzon syndrome-acanthosis nigricans syndrome;C4048328:Cervical cancer Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 21, 2021 | - - |
Craniosynostosis syndrome Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 30, 2015 | - - |
Hypochondroplasia Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Abnormality of the nervous system Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Kariminejad - Najmabadi Pathology & Genetics Center | Jul 10, 2021 | - - |
Saethre-Chotzen syndrome Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2009 | - - |
not specified Other:1
| not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Achondroplasia;C0410529:Hypochondroplasia;C1864436:Muenke syndrome;C1868678:Thanatophoric dysplasia type 1;C2677099:Crouzon syndrome-acanthosis nigricans syndrome Other:1
| not provided, no classification provided | phenotyping only | GenomeConnect - Invitae Patient Insights Network | - | Variant interpreted as Pathogenic and reported on 02-18-2019 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
D;T;.;.;T;.;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T;.;T
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Benign
L;.;L;L;.;L;.
MutationTaster
Benign
A;A;A;A;A;A
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D;.;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D;D;.;D;D
Sift4G
Benign
T;T;T;T;D;T;D
Polyphen
D;D;B;D;.;D;.
Vest4
MutPred
Loss of glycosylation at P250 (P = 0.0271);Loss of glycosylation at P250 (P = 0.0271);Loss of glycosylation at P250 (P = 0.0271);Loss of glycosylation at P250 (P = 0.0271);Loss of glycosylation at P250 (P = 0.0271);Loss of glycosylation at P250 (P = 0.0271);.;
MVP
MPC
0.35
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at