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NM_000142.5(FGFR3):c.1949A>T (p.Lys650Met) AND Hypochondroplasia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 29, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002310592.8

Allele description [Variation Report for NM_000142.5(FGFR3):c.1949A>T (p.Lys650Met)]

NM_000142.5(FGFR3):c.1949A>T (p.Lys650Met)

Gene:
FGFR3:fibroblast growth factor receptor 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_000142.5(FGFR3):c.1949A>T (p.Lys650Met)
HGVS:
  • NC_000004.12:g.1806163A>T
  • NG_012632.1:g.17852A>T
  • NM_000142.5:c.1949A>TMANE SELECT
  • NM_001163213.2:c.1955A>T
  • NM_001354809.2:c.1952A>T
  • NM_001354810.2:c.1952A>T
  • NM_022965.4:c.1613A>T
  • NP_000133.1:p.Lys650Met
  • NP_001156685.1:p.Lys652Met
  • NP_001341738.1:p.Lys651Met
  • NP_001341739.1:p.Lys651Met
  • NP_075254.1:p.Lys538Met
  • LRG_1021t1:c.1949A>T
  • LRG_1021:g.17852A>T
  • NC_000004.11:g.1807890A>T
  • NM_000142.3:c.1949A>T
  • NM_000142.4:c.1949A>T
  • NR_148971.2:n.2375A>T
  • P22607:p.Lys650Met
Protein change:
K538M; LYS650MET
Links:
UniProtKB: P22607#VAR_004161; OMIM: 134934.0015; dbSNP: rs121913105
NCBI 1000 Genomes Browser:
rs121913105
Molecular consequence:
  • NM_000142.5:c.1949A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001163213.2:c.1955A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354809.2:c.1952A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354810.2:c.1952A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022965.4:c.1613A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148971.2:n.2375A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Functional consequence:
Unknown function
Observations:
1

Condition(s)

Name:
Hypochondroplasia (HCH)
Identifiers:
MONDO: MONDO:0007793; MedGen: C0410529; Orphanet: 429; OMIM: 146000

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002601621Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 29, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV002601621.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 24, 2024