NM_000141.5(FGFR2):c.23T>G (p.Ile8Ser) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: Feb 24, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000756160.7

Allele description [Variation Report for NM_000141.5(FGFR2):c.23T>G (p.Ile8Ser)]

NM_000141.5(FGFR2):c.23T>G (p.Ile8Ser)

Gene:
FGFR2:fibroblast growth factor receptor 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q26.13
Genomic location:
Preferred name:
NM_000141.5(FGFR2):c.23T>G (p.Ile8Ser)
HGVS:
  • NC_000010.11:g.121593795A>C
  • NG_012449.2:g.9664T>G
  • NM_000141.5:c.23T>GMANE SELECT
  • NM_001144913.1:c.23T>G
  • NM_001144914.1:c.23T>G
  • NM_001144915.2:c.23T>G
  • NM_001144916.2:c.23T>G
  • NM_001144917.2:c.23T>G
  • NM_001144918.2:c.23T>G
  • NM_001144919.2:c.23T>G
  • NM_001320658.2:c.23T>G
  • NM_022970.3:c.23T>G
  • NM_023029.2:c.23T>G
  • NP_000132.3:p.Ile8Ser
  • NP_000132.3:p.Ile8Ser
  • NP_001138385.1:p.Ile8Ser
  • NP_001138386.1:p.Ile8Ser
  • NP_001138387.1:p.Ile8Ser
  • NP_001138388.1:p.Ile8Ser
  • NP_001138389.1:p.Ile8Ser
  • NP_001138390.1:p.Ile8Ser
  • NP_001138391.1:p.Ile8Ser
  • NP_001307587.1:p.Ile8Ser
  • NP_075259.4:p.Ile8Ser
  • NP_075418.1:p.Ile8Ser
  • LRG_994t1:c.23T>G
  • LRG_994t2:c.23T>G
  • LRG_994:g.9664T>G
  • LRG_994p1:p.Ile8Ser
  • LRG_994p2:p.Ile8Ser
  • NC_000010.10:g.123353309A>C
  • NM_000141.4:c.23T>G
  • NR_073009.2:n.656T>G
Protein change:
I8S
Links:
dbSNP: rs147307031
NCBI 1000 Genomes Browser:
rs147307031
Molecular consequence:
  • NM_000141.5:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144913.1:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144914.1:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144915.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144916.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144917.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144918.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144919.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320658.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022970.3:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_023029.2:c.23T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_073009.2:n.656T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000883886ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratoriescriteria provided, single submitter
Likely benign
(Mar 25, 2018)
germlineclinical testing

Citation Link,

SCV001869737GeneDxcriteria provided, single submitter
Benign
(Feb 24, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000883886.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.23T>G; p.Ile8Ser variant (rs147307031) has been reported in a patient with craniosynostosis; however, this patient also harbored another pathogenic variant, and the authors classified the p.Ile8Ser variant as “not pathogenic” (Goos 2015). This variant was also detected in a cohort of healthy individuals (Bodian 2014), is listed in the genome Aggregation Database (gnomAD) with an African population frequency of 0.3% (identified on 63 out of 24,026 chromosomes, including one homozygote) and is classified as benign in ClinVar (variant ID: 134388). The isoleucine at position 8 is weakly conserved, considering 12 species, and computational analyses of the effects of the p.Ile8Ser variant on protein structure and function make conflicting predictions (SIFT: damaging, PolyPhen-2: benign ). Based on the available information, the p.Ile8Ser variant is likely to be benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001869737.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is associated with the following publications: (PMID: 25425289)

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

Last Updated: Dec 4, 2021

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