NM_144997.7(FLCN):c.890_893del (p.Glu297fs) AND FLCN-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 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:: RCV003415852.4

Allele description [Variation Report for NM_144997.7(FLCN):c.890_893del (p.Glu297fs)]

NM_144997.7(FLCN):c.890_893del (p.Glu297fs)

Gene:

FLCN:folliculin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_144997.7(FLCN):c.890_893del (p.Glu297fs)

HGVS:

NC_000017.10:g.17122502_17122505del
NC_000017.11:g.17219190_17219193del
NG_008001.2:g.22998_23001del
NM_001353229.2:c.944_947del
NM_001353230.2:c.890_893del
NM_001353231.2:c.890_893del
NM_144997.6:c.890_893del
NM_144997.7:c.890_893delMANE SELECT
NP_001340158.1:p.Glu315fs
NP_001340159.1:p.Glu297fs
NP_001340160.1:p.Glu297fs
NP_659434.2:p.Glu297fs
LRG_325t1:c.890_893del
LRG_325:g.22998_23001del
NC_000017.10:g.17122502_17122505del
NC_000017.10:g.17122504_17122507del
NC_000017.10:g.17122504_17122507del
NC_000017.10:g.17122504_17122507delTTCT
NM_144997.5:c.890_893del
NM_144997.5:c.890_893delAAAG
p.[Glu297Alafs*25]

Protein change:

E297fs

Links:

dbSNP: rs398124541

NCBI 1000 Genomes Browser:

rs398124541

Molecular consequence:

NM_001353229.2:c.944_947del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353230.2:c.890_893del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353231.2:c.890_893del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_144997.7:c.890_893del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: FLCN-related disorder
Synonyms:: FLCN-related condition
Identifiers:

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RecName: Full=Stimulated by retinoic acid gene 8 protein homolog
RecName: Full=Stimulated by retinoic acid gene 8 protein homolog
gi|74713759|sp|Q7Z7C7.1|STRA8_HUMAN

Protein
LOC107495071 [Arachis duranensis]
LOC107495071 [Arachis duranensis]
Gene ID:107495071

Gene
LOC107458877 [Arachis duranensis]
LOC107458877 [Arachis duranensis]
Gene ID:107458877

Gene
LCTL [Vulpes vulpes]
LCTL [Vulpes vulpes]
Gene ID:112929670

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004118653	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 1, 2022)	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

SCV004118653

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 1, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 PreventionGenetics, part of Exact Sciences, SCV004118653.1

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

Description

The FLCN c.890_893delAAAG variant is predicted to result in a frameshift and premature protein termination (p.Glu297Alafs*25). In the literature, this variant is also referred to as c.1388_1391delAAAG (p.Glu297Alafs*321). This variant has been reported in individuals with Birt-Hogg-Dub syndrome (Kluger et al. 2009. PubMed ID: 19785621; Dow et al. 2016. PubMed ID: 27643397; Sprague et al. 2016. PubMed ID: 27470329). This variant, in the heterozygous state, was also reported in an individual who presented with isolated renal cell carcinoma and later developed pulmonary features (Patient 2, Woodward et al. 2008. PubMed ID: 18794106) and in another individual with colorectal cancer (Dobbins et al. 2016. PubMed ID: 27356891). This variant is reported in 0.0018% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-17122501-GCTTT-G). Frameshift variants in FLCN are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Nov 3, 2024

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