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NM_023110.3(FGFR1):c.320C>T (p.Ser107Leu) AND Hypogonadotropic hypogonadism 2 with or without anosmia

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 27, 2017
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:
RCV000300152.5

Allele description [Variation Report for NM_023110.3(FGFR1):c.320C>T (p.Ser107Leu)]

NM_023110.3(FGFR1):c.320C>T (p.Ser107Leu)

Gene:
FGFR1:fibroblast growth factor receptor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p11.23
Genomic location:
Preferred name:
NM_023110.3(FGFR1):c.320C>T (p.Ser107Leu)
HGVS:
  • NC_000008.11:g.38429720G>A
  • NG_007729.1:g.44115C>T
  • NM_001174063.2:c.320C>T
  • NM_001174064.2:c.296C>T
  • NM_001174065.2:c.320C>T
  • NM_001174066.2:c.92-1285C>T
  • NM_001174067.2:c.419C>T
  • NM_001354367.2:c.320C>T
  • NM_001354368.2:c.92-1285C>T
  • NM_001354369.2:c.320C>T
  • NM_001354370.2:c.92-1285C>T
  • NM_015850.4:c.320C>T
  • NM_023105.3:c.92-1285C>T
  • NM_023106.3:c.92-1285C>T
  • NM_023110.3:c.320C>TMANE SELECT
  • NP_001167534.1:p.Ser107Leu
  • NP_001167535.1:p.Ser99Leu
  • NP_001167536.1:p.Ser107Leu
  • NP_001167538.1:p.Ser140Leu
  • NP_001341296.1:p.Ser107Leu
  • NP_001341298.1:p.Ser107Leu
  • NP_056934.2:p.Ser107Leu
  • NP_075598.2:p.Ser107Leu
  • NP_075598.2:p.Ser107Leu
  • LRG_993t1:c.320C>T
  • LRG_993:g.44115C>T
  • LRG_993p1:p.Ser107Leu
  • NC_000008.10:g.38287238G>A
  • NM_023110.2:c.320C>T
Protein change:
S107L
Links:
dbSNP: rs140382957
NCBI 1000 Genomes Browser:
rs140382957
Molecular consequence:
  • NM_001174066.2:c.92-1285C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354368.2:c.92-1285C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354370.2:c.92-1285C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_023105.3:c.92-1285C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_023106.3:c.92-1285C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001174063.2:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174064.2:c.296C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174065.2:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174067.2:c.419C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354367.2:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354369.2:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015850.4:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_023110.3:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypogonadotropic hypogonadism 2 with or without anosmia (HH2)
Synonyms:
Kallmann syndrome 2; HYPOGONADOTROPIC HYPOGONADISM 2 WITHOUT ANOSMIA; HYPOGONADOTROPIC HYPOGONADISM 2 WITH OR WITHOUT ANOSMIA, SUSCEPTIBILITY TO; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007844; MedGen: C1563720; Orphanet: 478; OMIM: 147950

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000473686Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Apr 27, 2017) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Submicroscopic deletion involving the fibroblast growth factor receptor 1 gene in a patient with combined pituitary hormone deficiency.

Fukami M, Iso M, Sato N, Igarashi M, Seo M, Kazukawa I, Kinoshita E, Dateki S, Ogata T.

Endocr J. 2013;60(8):1013-20. Epub 2013 May 9.

PubMed [citation]
PMID:
23657145

Exome sequencing for the diagnosis of 46,XY disorders of sex development.

Baxter RM, Arboleda VA, Lee H, Barseghyan H, Adam MP, Fechner PY, Bargman R, Keegan C, Travers S, Schelley S, Hudgins L, Mathew RP, Stalker HJ, Zori R, Gordon OK, Ramos-Platt L, Pawlikowska-Haddal A, Eskin A, Nelson SF, Délot E, Vilain E.

J Clin Endocrinol Metab. 2015 Feb;100(2):E333-44. doi: 10.1210/jc.2014-2605. Epub 2014 Nov 10.

PubMed [citation]
PMID:
25383892
PMCID:
PMC4318895
See all PubMed Citations (6)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000473686.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Last Updated: Mar 16, 2024