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NM_023110.3(FGFR1):c.2122G>T (p.Glu708Ter) AND Hypogonadotropic hypogonadism 2 with or without anosmia

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
May 4, 2023
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:
RCV001542472.3

Allele description [Variation Report for NM_023110.3(FGFR1):c.2122G>T (p.Glu708Ter)]

NM_023110.3(FGFR1):c.2122G>T (p.Glu708Ter)

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.2122G>T (p.Glu708Ter)
HGVS:
  • NC_000008.11:g.38414216C>A
  • NG_007729.1:g.59619G>T
  • NM_001174063.2:c.2116G>T
  • NM_001174064.2:c.2092G>T
  • NM_001174065.2:c.2116G>T
  • NM_001174066.2:c.1855G>T
  • NM_001174067.2:c.2215G>T
  • NM_001354367.2:c.2116G>T
  • NM_001354368.2:c.1843G>T
  • NM_001354369.2:c.2110G>T
  • NM_001354370.2:c.1849G>T
  • NM_015850.4:c.2116G>T
  • NM_023105.3:c.1855G>T
  • NM_023106.3:c.1849G>T
  • NM_023110.2:c.2122G>T
  • NM_023110.3:c.2122G>TMANE SELECT
  • NP_001167534.1:p.Glu706Ter
  • NP_001167535.1:p.Glu698Ter
  • NP_001167536.1:p.Glu706Ter
  • NP_001167537.1:p.Glu619Ter
  • NP_001167538.1:p.Glu739Ter
  • NP_001341296.1:p.Glu706Ter
  • NP_001341297.1:p.Glu615Ter
  • NP_001341298.1:p.Glu704Ter
  • NP_001341299.1:p.Glu617Ter
  • NP_056934.2:p.Glu706Ter
  • NP_075593.1:p.Glu619Ter
  • NP_075594.1:p.Glu617Ter
  • NP_075598.2:p.Glu708Ter
  • LRG_993t1:c.2122G>T
  • LRG_993:g.59619G>T
  • NC_000008.10:g.38271734C>A
Protein change:
E615*
Links:
dbSNP: rs2150533516
NCBI 1000 Genomes Browser:
rs2150533516
Molecular consequence:
  • NM_001174063.2:c.2116G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001174064.2:c.2092G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001174065.2:c.2116G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001174066.2:c.1855G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001174067.2:c.2215G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354367.2:c.2116G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354368.2:c.1843G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354369.2:c.2110G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354370.2:c.1849G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015850.4:c.2116G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_023105.3:c.1855G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_023106.3:c.1849G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_023110.3:c.2122G>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001760209Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)		Likely pathogenicgermlineclinical testing

Citation Link,

SCV003932509Reproductive Endocrine Unit, Massachusetts General Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 4, 2023) 		unknownresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot provided1not providedresearch
not providedgermlineyesnot providednot 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 Genomics England Pilot Project, Genomics England, SCV001760209.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Reproductive Endocrine Unit, Massachusetts General Hospital, SCV003932509.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)

Description

The variant NM_023110.2:c.2122G>T, p.(Glu708*) het has been classified as P1c based on the variant meeting the following ACMG Criteria: PVS1,PM2,PP3.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023