ClinVar Genomic variation as it relates to human health
NM_000142.5(FGFR3):c.1949A>T (p.Lys650Met)
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.1949A>T (p.Lys650Met)
Variation ID: 16341 Accession: VCV000016341.16
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4p16.3 4: 1806163 (GRCh38) [ NCBI UCSC ] 4: 1807890 (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 Oct 1, 2013 Aug 25, 2024 Sep 29, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000142.5:c.1949A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000133.1:p.Lys650Met missense NM_001163213.2:c.1955A>T NP_001156685.1:p.Lys652Met missense NM_001354809.2:c.1952A>T NP_001341738.1:p.Lys651Met missense NM_001354810.2:c.1952A>T NP_001341739.1:p.Lys651Met missense NM_022965.4:c.1613A>T NP_075254.1:p.Lys538Met missense NR_148971.2:n.2375A>T non-coding transcript variant NC_000004.12:g.1806163A>T NC_000004.11:g.1807890A>T NG_012632.1:g.17852A>T LRG_1021:g.17852A>T LRG_1021t1:c.1949A>T P22607:p.Lys650Met - Protein change
- K650M, K652M, K538M, K651M
- Other names
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- Canonical SPDI
- NC_000004.12:1806162:A:T
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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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Unknown function
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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
Help
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
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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 (2) |
no assertion criteria provided
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Jan 15, 2008 | RCV000017750.39 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Jul 25, 2022 | RCV001574416.18 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 29, 2022 | RCV002310592.8 | |
Pathogenic (1) |
criteria provided, single submitter
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May 31, 2022 | RCV002496392.8 | |
Pathogenic (1) |
no assertion criteria provided
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Jan 15, 2008 | RCV004558267.1 |
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
Help
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
Help
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
(Jul 29, 2020)
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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: SCV001801232.1
First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
Comment:
Published functional studies demonstrate significantly increased receptor kinase activity compared to wild type (Tavormina et al., 1999; Krejci et al., 2008); Not observed in large … (more)
Published functional studies demonstrate significantly increased receptor kinase activity compared to wild type (Tavormina et al., 1999; Krejci et al., 2008); Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 10053006, 30782830, 18076102, 9207791, 27214123, 10671061, 25119967, 19088846, 19039991, 25614871, 9857065, 10377013, 29242050, 29030113, 29360984, 22045636, 20301540, 30048571, 29542187, 30168875, 29068064) (less)
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Pathogenic
(Sep 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hypochondroplasia
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV002601621.1
First in ClinVar: Nov 19, 2022 Last updated: Nov 19, 2022 |
Comment:
A heterozygous missense variation in exon 14 of the FGFR3 gene that results in the amino acid substitution of Methionine for Lysine at codon 650 … (more)
A heterozygous missense variation in exon 14 of the FGFR3 gene that results in the amino acid substitution of Methionine for Lysine at codon 650 was detected . The p.Lys650Met variant has not been reported in the 1000 genomes, gnomAD and our internal databases. The in silico predictions of the variant are probably damaging by PolyPhen-2 (HumDiv), damaging by SIFT, LRT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a pathogenic. (less)
Clinical Features:
Skeletal dysplasia (present)
Sex: female
Method: DNA was used to perform targeted gene capture using a custom capture kit. Libraries were sequenced to mean >80-100X coverage on Illumina sequencing platform. Sequence obtained were aligned to human references genome using BWA program and analyzed using Picard and GATK-Lite toolkit to identify variants in the targeted genes relevant to clinical indication.
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Pathogenic
(May 31, 2022)
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criteria provided, single submitter
Method: clinical testing
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Achondroplasia
Malignant tumor of urinary bladder Colorectal cancer Hypochondroplasia LADD syndrome 1 Epidermal nevus Thanatophoric dysplasia type 1 Thanatophoric dysplasia, type 2 Germ cell tumor of testis Muenke syndrome Cervical cancer Camptodactyly-tall stature-scoliosis-hearing loss syndrome Crouzon syndrome-acanthosis nigricans syndrome Severe achondroplasia-developmental delay-acanthosis nigricans syndrome
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002808080.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Feb 05, 2018)
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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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Blueprint Genetics
Accession: SCV001832244.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021
Comment:
Patient analyzed with Comprehensive Skeletal Dysplasias and Disorders Panel
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Pathogenic
(Jul 25, 2022)
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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: SCV002507707.3
First in ClinVar: May 16, 2022 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Lys650 amino acid residue in FGFR3. Other variant(s) that disrupt this … (more)
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Lys650 amino acid residue in FGFR3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17875876, 26818779). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects FGFR3 function (PMID: 9857065, 19088846). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 16341). This missense change has been observed in individual(s) with severe achondroplasia with developmental delay and acanthosis nigricans (PMID: 10053006, 18076102). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with methionine, which is neutral and non-polar, at codon 650 of the FGFR3 protein (p.Lys650Met). (less)
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Pathogenic
(Jul 13, 2022)
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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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Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005197932.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
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Pathogenic
(Jan 15, 2008)
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no assertion criteria provided
Method: literature only
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THANATOPHORIC DYSPLASIA, TYPE I
Affected status: not provided
Allele origin:
unknown
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OMIM
Accession: SCV000038028.3
First in ClinVar: Apr 04, 2013 Last updated: Jul 25, 2016 |
Comment on evidence:
In 2 unrelated patients, Francomano et al. (1996) found the same novel FGFR3 mutation as the cause of a previously undescribed skeletal dysplasia characterized by … (more)
In 2 unrelated patients, Francomano et al. (1996) found the same novel FGFR3 mutation as the cause of a previously undescribed skeletal dysplasia characterized by extreme short stature, severe tibial bowing, profound developmental delay, and acanthosis nigricans (SADDAN; 616482). The mutation, a 1949A-T transversion causing a lys650-to-met (K650M) substitution, occurs in the distal tyrosine kinase domain. (A change at the adjacent nucleotide in FGFR3 (1948A-G) causes a substitution at the same codon (K650E; 134934.0004) and results in thanatophoric dysplasia type II (187601).) Both individuals with the K650M mutation, one aged 5 years and the other aged 29 years, had skeletal findings distinct from both TD1 (187600) and TD2. These included absence of craniosynostosis or cloverleaf skull anomaly and presence of moderate bowing of the femurs with reverse bowing of the tibia and fibula. The older patient had bilateral tibial pseudoarthroses. Other clinical and physical features common to both patients included survival past infancy; periods of respiratory compromise during infancy but without the need for prolonged mechanical ventilation; development of acanthosis nigricans in the cervical and flexural areas; and seizures and hydrocephalus during infancy with severe limitation of motor and intellectual development. The younger patient had structural anomalies of the brain, including a hypoplastic corpus callosum and abnormal development of the cerebellum. Tavormina et al. (1999) referred to the distinctive syndrome described by Francomano et al. (1996) as SADDAN dysplasia, an acronym derived from 'severe achondroplasia with developmental delay and acanthosis nigricans.' They reported 4 unrelated individuals with this syndrome (2 of whom were reported by Francomano et al., 1996) approaching the severity observed in thanatophoric dysplasia type I. Different from thanatophoric dysplasia was the development of extensive areas of acanthosis nigricans beginning in early childhood in 3 patients, severe neurologic impairments, and survival past infancy without prolonged life-support measures. Lys650 is highly conserved in the kinase domain activation loop. Transient transfection studies with FGFR3 mutant constructs showed that the lys650-to-met mutation caused a dramatic increase in constitutive receptor kinase activity, approximately 3 times greater than that observed with the lys650-to-glu mutation. Zankl et al. (2008) reported a patient with the SADDAN phenotype associated with a K650M substitution resulting from a de novo 1949A-T transversion in exon 15 of the FGFR3 gene. The patient had severe micromelia, frontal bossing, large anterior fontanel, depressed nasal bridge, reverse tibial bowing, small thorax, and hypotonia. Acanthosis nigricans was not present. He died at age 21 days due to respiratory failure. Zankl et al. (2008) noted that about half of patients reported with the K650M mutation died before 21 days of age, while others have shown longer survival. The authors also noted that acanthosis nigricans has been reported in patients with other skeletal dysplasias due to FGFR3 mutations, and thus should be considered a long-term complication rather than a specific feature of SADDAN. In addition, mental retardation only becomes apparent in long-term survivors and thus cannot be used as a diagnostic criterion for SADDAN in the neonatal period. The K650M mutation due to a 1988A-T transversion was found in cell lines and tumors of multiple myeloma (254500) containing a karyotypically silent translocation between t(4;14) and the IgH. Chesi et al. (1997) proposed that after the t(4;14) translocation, somatic mutation during tumor progression generated an FGFR3 protein that was active in the absence of ligand. FGFR is, then, another example of a gene that can be both an oncogene and a 'teratogene.' Kitoh et al. (1998) reported the lys650-to-met mutation as the cause of thanatophoric dysplasia type I. (less)
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Pathogenic
(Jan 15, 2008)
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no assertion criteria provided
Method: literature only
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ACHONDROPLASIA, SEVERE, WITH DEVELOPMENTAL DELAY AND ACANTHOSIS NIGRICANS
Affected status: not provided
Allele origin:
unknown
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OMIM
Accession: SCV000038027.4
First in ClinVar: Apr 04, 2013 Last updated: Jun 09, 2024 |
Comment on evidence:
In 2 unrelated patients, Francomano et al. (1996) found the same novel FGFR3 mutation as the cause of a previously undescribed skeletal dysplasia characterized by … (more)
In 2 unrelated patients, Francomano et al. (1996) found the same novel FGFR3 mutation as the cause of a previously undescribed skeletal dysplasia characterized by extreme short stature, severe tibial bowing, profound developmental delay, and acanthosis nigricans (SADDAN; 616482). The mutation, a 1949A-T transversion causing a lys650-to-met (K650M) substitution, occurs in the distal tyrosine kinase domain. (A change at the adjacent nucleotide in FGFR3 (1948A-G) causes a substitution at the same codon (K650E; 134934.0004) and results in thanatophoric dysplasia type II (187601).) Both individuals with the K650M mutation, one aged 5 years and the other aged 29 years, had skeletal findings distinct from both TD1 (187600) and TD2. These included absence of craniosynostosis or cloverleaf skull anomaly and presence of moderate bowing of the femurs with reverse bowing of the tibia and fibula. The older patient had bilateral tibial pseudoarthroses. Other clinical and physical features common to both patients included survival past infancy; periods of respiratory compromise during infancy but without the need for prolonged mechanical ventilation; development of acanthosis nigricans in the cervical and flexural areas; and seizures and hydrocephalus during infancy with severe limitation of motor and intellectual development. The younger patient had structural anomalies of the brain, including a hypoplastic corpus callosum and abnormal development of the cerebellum. Tavormina et al. (1999) referred to the distinctive syndrome described by Francomano et al. (1996) as SADDAN dysplasia, an acronym derived from 'severe achondroplasia with developmental delay and acanthosis nigricans.' They reported 4 unrelated individuals with this syndrome (2 of whom were reported by Francomano et al., 1996) approaching the severity observed in thanatophoric dysplasia type I. Different from thanatophoric dysplasia was the development of extensive areas of acanthosis nigricans beginning in early childhood in 3 patients, severe neurologic impairments, and survival past infancy without prolonged life-support measures. Lys650 is highly conserved in the kinase domain activation loop. Transient transfection studies with FGFR3 mutant constructs showed that the lys650-to-met mutation caused a dramatic increase in constitutive receptor kinase activity, approximately 3 times greater than that observed with the lys650-to-glu mutation. Zankl et al. (2008) reported a patient with the SADDAN phenotype associated with a K650M substitution resulting from a de novo 1949A-T transversion in exon 15 of the FGFR3 gene. The patient had severe micromelia, frontal bossing, large anterior fontanel, depressed nasal bridge, reverse tibial bowing, small thorax, and hypotonia. Acanthosis nigricans was not present. He died at age 21 days due to respiratory failure. Zankl et al. (2008) noted that about half of patients reported with the K650M mutation died before 21 days of age, while others have shown longer survival. The authors also noted that acanthosis nigricans has been reported in patients with other skeletal dysplasias due to FGFR3 mutations, and thus should be considered a long-term complication rather than a specific feature of SADDAN. In addition, mental retardation only becomes apparent in long-term survivors and thus cannot be used as a diagnostic criterion for SADDAN in the neonatal period. The K650M mutation due to a 1988A-T transversion was found in cell lines and tumors of multiple myeloma (254500) containing a karyotypically silent translocation between t(4;14) and the IgH. Chesi et al. (1997) proposed that after the t(4;14) translocation, somatic mutation during tumor progression generated an FGFR3 protein that was active in the absence of ligand. FGFR is, then, another example of a gene that can be both an oncogene and a 'teratogene.' Kitoh et al. (1998) reported the lys650-to-met mutation as the cause of thanatophoric dysplasia type I. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Thanatophoric dysplasia type 1
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000086709.2
First in ClinVar: Oct 01, 2013 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
Help
A brief description of the result of this method for this variant. |
Submitter
Help
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
Help
This column includes more information supporting functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Unknown function
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV002601621.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Thanatophoric Dysplasia. | Adam MP | - | 2023 | PMID: 20301540 |
Effective treatment by glycolic acid peeling for cutaneous manifestation of familial generalized acanthosis nigricans caused by FGFR3 mutation. | Ichiyama S | Journal of the European Academy of Dermatology and Venereology : JEADV | 2016 | PMID: 26818779 |
Analysis of STAT1 activation by six FGFR3 mutants associated with skeletal dysplasia undermines dominant role of STAT1 in FGFR3 signaling in cartilage. | Krejci P | PloS one | 2008 | PMID: 19088846 |
Prenatal and postnatal presentation of severe achondroplasia with developmental delay and acanthosis nigricans (SADDAN) due to the FGFR3 Lys650Met mutation. | Zankl A | American journal of medical genetics. Part A | 2008 | PMID: 18076102 |
Familial acanthosis nigricans due to K650T FGFR3 mutation. | Berk DR | Archives of dermatology | 2007 | PMID: 17875876 |
A novel skeletal dysplasia with developmental delay and acanthosis nigricans is caused by a Lys650Met mutation in the fibroblast growth factor receptor 3 gene. | Tavormina PL | American journal of human genetics | 1999 | PMID: 10053006 |
Lys650Met substitution in the tyrosine kinase domain of the fibroblast growth factor receptor gene causes thanatophoric dysplasia Type I. Mutations in brief no. 199. Online. | Kitoh H | Human mutation | 1998 | PMID: 10671061 |
Effect of transmembrane and kinase domain mutations on fibroblast growth factor receptor 3 chimera signaling in PC12 cells. A model for the control of receptor tyrosine kinase activation. | Raffioni S | The Journal of biological chemistry | 1998 | PMID: 9857065 |
Frequent translocation t(4;14)(p16.3;q32.3) in multiple myeloma is associated with increased expression and activating mutations of fibroblast growth factor receptor 3. | Chesi M | Nature genetics | 1997 | PMID: 9207791 |
Francomano, C. A., Bellus, G. A., Szabo, J., McIntosh, I., Dorst, J., Lee, R., Hurko, O., Fraley, A. E., Bamshad, M. J. A new skeletal dysplasia with severe tibial bowing, profound developmental delay and acanthosis nigricans is caused by a Lys 650 Met mutation in fibroblast growth factor receptor 3 (FGFR3). (Abstract) Am. J. Hum. Genet. 59 (suppl.): A25-only, 1996. | - | - | - | - |
Text-mined citations for rs121913105 ...
HelpRecord last updated Nov 25, 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.