ClinVar Genomic variation as it relates to human health
NM_000142.5(FGFR3):c.1948A>C (p.Lys650Gln)
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.1948A>C (p.Lys650Gln)
Variation ID: 16348 Accession: VCV000016348.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4p16.3 4: 1806162 (GRCh38) [ NCBI UCSC ] 4: 1807889 (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 Nov 24, 2024 Oct 10, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000142.5:c.1948A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000133.1:p.Lys650Gln missense NM_001163213.2:c.1954A>C NP_001156685.1:p.Lys652Gln missense NM_001354809.2:c.1951A>C NP_001341738.1:p.Lys651Gln missense NM_001354810.2:c.1951A>C NP_001341739.1:p.Lys651Gln missense NM_022965.4:c.1612A>C NP_075254.1:p.Lys538Gln missense NR_148971.2:n.2374A>C non-coding transcript variant NC_000004.12:g.1806162A>C NC_000004.11:g.1807889A>C NG_012632.1:g.17851A>C LRG_1021:g.17851A>C LRG_1021t1:c.1948A>C LRG_1021p1:p.Lys650Gln LRG_1021t2:c.1954A>C LRG_1021p2:p.Lys652Gln P22607:p.Lys650Gln - Protein change
- K650Q, K652Q, K651Q, K538Q
- Other names
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- Canonical SPDI
- NC_000004.12:1806161:A: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
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
- Links
- Comment on variant
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
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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 (6) |
criteria provided, multiple submitters, no conflicts
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Oct 10, 2024 | RCV000017757.48 | |
Pathogenic (1) |
no assertion criteria provided
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Dec 15, 2007 | RCV000144153.12 | |
Likely pathogenic (1) |
no assertion criteria provided
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May 13, 2016 | RCV000430843.9 | |
Likely pathogenic (1) |
no assertion criteria provided
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Jul 14, 2015 | RCV000437923.9 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 9, 2023 | RCV002228032.14 |
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
(Jun 02, 2023)
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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: SCV001136685.2
First in ClinVar: Jan 09, 2020 Last updated: Jun 10, 2023 |
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Pathogenic
(Aug 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: SCV000640367.6
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 650 of the FGFR3 protein (p.Lys650Gln). … (more)
This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 650 of the FGFR3 protein (p.Lys650Gln). This variant is present in population databases (rs78311289, gnomAD 0.007%). This missense change has been observed in individual(s) with hypochondroplasia with or without acanthosis nigricans and/or hyperinsulinemia (PMID: 11055896, 16912704, 20453470, 21510009). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 16348). 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. Experimental studies have shown that this missense change affects FGFR3 function (PMID: 11055896). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Dec 22, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hypochondroplasia
Affected status: yes
Allele origin:
germline
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Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV005090993.1
First in ClinVar: Aug 04, 2024 Last updated: Aug 04, 2024 |
Comment:
PS4, PM1, PM2, PM5, PP3, PP5 - The variant has been reported in ClinVar as Pathogenic by other laboratories (Variation ID 16348). This missense change … (more)
PS4, PM1, PM2, PM5, PP3, PP5 - The variant has been reported in ClinVar as Pathogenic by other laboratories (Variation ID 16348). This missense change has been observed in individual(s) with hypochondroplasia with or without acanthosis nigricans and/or hyperinsulinemia (PMID: 20453470). (less)
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Pathogenic
(Oct 10, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hypochondroplasia
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV005399778.1
First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.5, 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, 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, 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, 16501574). (I) 0200 - Variant is predicted to result in a missense amino acid change from lysine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v4) <0.01 (2 heterozygotes, 0 homozygote). (SP) 0309 - Multiple alternative amino acid changes at the same position have been observed in gnomAD (v4) (4 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated protein tyrosine and serine/threonine kinase domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by clinical laboratories. This variant has also been observed in multiple unrelated heterozygous individuals with hypochondroplasia and acanthosis nigricans, as well as hyperinsulinemia in one case (PMID: 31708465, 30168875, 21510009, 16912704, 18000903, 20453470, 11055896). (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Jan 23, 2015)
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no assertion criteria provided
Method: clinical testing
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Hypochondroplasia
Affected status: yes
Allele origin:
germline
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Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital
Accession: SCV000692268.1
First in ClinVar: Feb 19, 2018 Last updated: Feb 19, 2018 |
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Likely pathogenic
(Jul 14, 2015)
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no assertion criteria provided
Method: literature only
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Urinary bladder carcinoma
(Somatic mutation)
Affected status: yes
Allele origin:
somatic
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Database of Curated Mutations (DoCM)
Accession: SCV000505531.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
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Likely pathogenic
(May 13, 2016)
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no assertion criteria provided
Method: literature only
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Acanthosis nigricans
(Somatic mutation)
Affected status: yes
Allele origin:
somatic
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Database of Curated Mutations (DoCM)
Accession: SCV000510405.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
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Pathogenic
(Dec 15, 2007)
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no assertion criteria provided
Method: literature only
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HYPOCHONDROPLASIA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000038035.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 23, 2017 |
Comment on evidence:
Bellus et al. (2000) identified a 1948A-C transversion in the FGFR3 gene, predicting a lys650-to-gln (K650Q) amino acid substitution and causing hypochondroplasia (146000) in a … (more)
Bellus et al. (2000) identified a 1948A-C transversion in the FGFR3 gene, predicting a lys650-to-gln (K650Q) amino acid substitution and causing hypochondroplasia (146000) in a form milder than that seen in individuals with the asn540-to-lys (134934.0010) or lys650-to-met (134934.0015) mutations. Heuertz et al. (2006) identified the K560Q mutation in a patient with a moderate form of hypochondroplasia. Leroy et al. (2007) identified the K650Q mutation in a patient with a mild form of hypochondroplasia who was also diagnosed with acanthosis nigricans at 8 years of age. Leroy et al. (2007) stated that the mutation is located in the second part (3-prime side) of the split tyrosine kinase domain in the intracellular portion of the single-pass transmembrane of the receptor and that it unfavorably modulates the receptor's physiologic downstream inhibitory signaling. Sibley et al. (2001) found the same mutation, which they designated LYS652GLN (K652Q), in a transitional cell carcinoma of the bladder (109800). (less)
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Pathogenic
(Dec 15, 2007)
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no assertion criteria provided
Method: literature only
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BLADDER CANCER, SOMATIC
Affected status: not provided
Allele origin:
somatic
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OMIM
Accession: SCV000189233.2
First in ClinVar: Sep 25, 2014 Last updated: Oct 23, 2017 |
Comment on evidence:
Bellus et al. (2000) identified a 1948A-C transversion in the FGFR3 gene, predicting a lys650-to-gln (K650Q) amino acid substitution and causing hypochondroplasia (146000) in a … (more)
Bellus et al. (2000) identified a 1948A-C transversion in the FGFR3 gene, predicting a lys650-to-gln (K650Q) amino acid substitution and causing hypochondroplasia (146000) in a form milder than that seen in individuals with the asn540-to-lys (134934.0010) or lys650-to-met (134934.0015) mutations. Heuertz et al. (2006) identified the K560Q mutation in a patient with a moderate form of hypochondroplasia. Leroy et al. (2007) identified the K650Q mutation in a patient with a mild form of hypochondroplasia who was also diagnosed with acanthosis nigricans at 8 years of age. Leroy et al. (2007) stated that the mutation is located in the second part (3-prime side) of the split tyrosine kinase domain in the intracellular portion of the single-pass transmembrane of the receptor and that it unfavorably modulates the receptor's physiologic downstream inhibitory signaling. Sibley et al. (2001) found the same mutation, which they designated LYS652GLN (K652Q), in a transitional cell carcinoma of the bladder (109800). (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: SCV000086723.3
First in ClinVar: Oct 01, 2013 Last updated: Oct 01, 2022 |
Comment:
Greater likelihood of developing acanthosis nigricans [Berk et al 2010, Blomberg et al 2010]
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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 |
Mild osteochondrodysplasia with acanthosis nigricans in a short-statured Taiwanese family due to the p.Lys650Gln mutation in FGFR3. | Lin WD | Pediatrics and neonatology | 2019 | PMID: 31708465 |
Familial acanthosis nigricans with the FGFR3 mutation: Differences of pigmentation between male and female patients. | Yasuda M | The Journal of dermatology | 2018 | PMID: 30168875 |
Muenke syndrome: An international multicenter natural history study. | Kruszka P | American journal of medical genetics. Part A | 2016 | PMID: 26740388 |
FGFR3 mutation frequency in 324 cases from the International Skeletal Dysplasia Registry. | Xue Y | Molecular genetics & genomic medicine | 2014 | PMID: 25614871 |
Prospective enterprise-level molecular genotyping of a cohort of cancer patients. | MacConaill LE | The Journal of molecular diagnostics : JMD | 2014 | PMID: 25157968 |
A novel homozygous mutation in FGFR3 causes tall stature, severe lateral tibial deviation, scoliosis, hearing impairment, camptodactyly, and arachnodactyly. | Makrythanasis P | Human mutation | 2014 | PMID: 24864036 |
Acanthosis nigricans and hypochondroplasia in a child with a K650Q mutation in FGFR3. | Berk DR | Pediatric dermatology | 2010 | PMID: 21510009 |
FGFR3 mutations and the skin: report of a patient with a FGFR3 gene mutation, acanthosis nigricans, hypochondroplasia and hyperinsulinemia and review of the literature. | Blomberg M | Dermatology (Basel, Switzerland) | 2010 | PMID: 20453470 |
Muenke syndrome (FGFR3-related craniosynostosis): expansion of the phenotype and review of the literature. | Doherty ES | American journal of medical genetics. Part A | 2007 | PMID: 18000976 |
Acanthosis nigricans in a child with mild osteochondrodysplasia and K650Q mutation in the FGFR3 gene. | Leroy JG | American journal of medical genetics. Part A | 2007 | PMID: 18000903 |
Novel FGFR3 mutations creating cysteine residues in the extracellular domain of the receptor cause achondroplasia or severe forms of hypochondroplasia. | Heuertz S | European journal of human genetics : EJHG | 2006 | PMID: 16912704 |
Mutations in different components of FGF signaling in LADD syndrome. | Rohmann E | Nature genetics | 2006 | PMID: 16501574 |
Loss of heterozygosity at 4p16.3 and mutation of FGFR3 in transitional cell carcinoma. | Sibley K | Oncogene | 2001 | PMID: 11314002 |
Distinct missense mutations of the FGFR3 lys650 codon modulate receptor kinase activation and the severity of the skeletal dysplasia phenotype. | Bellus GA | American journal of human genetics | 2000 | PMID: 11055896 |
http://docm.genome.wustl.edu/variants/ENST00000260795:c.1948A>C | - | - | - | - |
http://docm.genome.wustl.edu/variants/ENST00000340107:c.1954A>C | - | - | - | - |
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Text-mined citations for rs78311289 ...
HelpRecord last updated Nov 30, 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.
NCBI staff reviewed the sequence information reported in PubMed 11314002 Fig. 1C to determine the location of this allele on the current reference sequence.