NM_023110.3(FGFR1):c.1711del (p.Glu571fs) AND Hypogonadotropic hypogonadism 2 with or without anosmia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 13, 2014
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:: RCV000449624.1

Allele description [Variation Report for NM_023110.3(FGFR1):c.1711del (p.Glu571fs)]

NM_023110.3(FGFR1):c.1711del (p.Glu571fs)

Gene:

FGFR1:fibroblast growth factor receptor 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8p11.23

Genomic location:

Preferred name:

NM_023110.3(FGFR1):c.1711del (p.Glu571fs)

HGVS:

NC_000008.11:g.38416015del
NG_007729.1:g.57822del
NM_001174063.2:c.1705del
NM_001174064.2:c.1681del
NM_001174065.2:c.1705del
NM_001174066.2:c.1444del
NM_001174067.2:c.1804del
NM_001354367.2:c.1705del
NM_001354368.2:c.1432del
NM_001354369.2:c.1699del
NM_001354370.2:c.1438del
NM_015850.4:c.1705del
NM_023105.3:c.1444del
NM_023106.3:c.1438del
NM_023110.3:c.1711delMANE SELECT
NP_001167534.1:p.Glu569fs
NP_001167535.1:p.Glu561fs
NP_001167536.1:p.Glu569fs
NP_001167537.1:p.Glu482fs
NP_001167538.1:p.Glu602fs
NP_001341296.1:p.Glu569fs
NP_001341297.1:p.Glu478fs
NP_001341298.1:p.Glu567fs
NP_001341299.1:p.Glu480fs
NP_056934.2:p.Glu569fs
NP_075593.1:p.Glu482fs
NP_075594.1:p.Glu480fs
NP_075598.2:p.Glu571fs
LRG_993:g.57822del
NC_000008.10:g.38273533del
NM_023105.2:c.1444delG
p.Glu482Serfs*61

Protein change:

E478fs

Links:

dbSNP: rs1060499663

NCBI 1000 Genomes Browser:

rs1060499663

Molecular consequence:

NM_001174063.2:c.1705del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174064.2:c.1681del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174065.2:c.1705del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174066.2:c.1444del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174067.2:c.1804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354367.2:c.1705del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354368.2:c.1432del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354369.2:c.1699del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354370.2:c.1438del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015850.4:c.1705del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023105.3:c.1444del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023106.3:c.1438del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023110.3:c.1711del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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Profile neighbors for GEO Profiles (Select 8312903) (199)
GEO Profiles
PREDICTED: Homo sapiens enoyl-CoA hydratase domain containing 2 (ECHDC2), transc...
PREDICTED: Homo sapiens enoyl-CoA hydratase domain containing 2 (ECHDC2), transcript variant X6, mRNA
gi|2217268800|ref|XM_047424344.1|

Nucleotide
Concise Conserved Domain Links for Protein (Select 109948279) (1)
Conserved Domains
Taxonomy Links for PopSet (Select 485650937) (286)
Taxonomy
IL6ST interleukin 6 cytokine family signal transducer [Homo sapiens]
IL6ST interleukin 6 cytokine family signal transducer [Homo sapiens]
Gene ID:3572

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000537726	Center of Genomic medicine, Geneva, University Hospital of Geneva	criteria provided, single submitter (MacArthur et al. (Nature 2014))	Pathogenic (Oct 13, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000537726

Center of Genomic medicine, Geneva, University Hospital of Geneva

criteria provided, single submitter

(MacArthur et al. (Nature 2014))

Pathogenic
(Oct 13, 2014)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Guidelines for investigating causality of sequence variants in human disease.

MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, et al.

Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127.

PubMed [citation]

PMID:: 24759409
PMCID:: PMC4180223

Details of each submission

From Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV000537726.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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