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NM_144997.7(FLCN):c.250-2A>G AND FLCN-related disorder

Germline classification:
Pathogenic (1 submission)
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:
RCV003421978.5

Allele description [Variation Report for NM_144997.7(FLCN):c.250-2A>G]

NM_144997.7(FLCN):c.250-2A>G

Gene:
FLCN:folliculin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p11.2
Genomic location:
Preferred name:
NM_144997.7(FLCN):c.250-2A>G
HGVS:
  • NC_000017.11:g.17226324T>C
  • NG_008001.2:g.15865A>G
  • NM_001353229.2:c.250-2A>G
  • NM_001353230.2:c.250-2A>G
  • NM_001353231.2:c.250-2A>G
  • NM_144606.7:c.250-2A>G
  • NM_144997.7:c.250-2A>GMANE SELECT
  • LRG_325t1:c.250-2A>G
  • LRG_325:g.15865A>G
  • NC_000017.10:g.17129638T>C
  • NM_144997.5:c.250-2A>G
  • NM_144997.6:c.250-2A>G
Nucleotide change:
IVS4AS, A-G, -2
Links:
OMIM: 607273.0014; dbSNP: rs398124533
NCBI 1000 Genomes Browser:
rs398124533
Molecular consequence:
  • NM_001353229.2:c.250-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001353230.2:c.250-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001353231.2:c.250-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_144606.7:c.250-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_144997.7:c.250-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004106650PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 4, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 PreventionGenetics, part of Exact Sciences, SCV004106650.1

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

Description

The FLCN c.250-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant is alternatively referred to as IVS4-2A>G in the literature. This variant was reported in individuals with Birt-Hogg-Dubé syndrome (Table 1, Toro et al. 2008. PubMed ID: 18234728; Figure 2, Sattler et al. 2020. PubMed ID: 31958439; Truong et al. 2021. PubMed ID: 34654685). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-17129638-T-C). It is interpreted as likely pathogenic and pathogenic in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/96481/). Variants that disrupt the consensus splice acceptor site in FLCN are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Oct 5, 2025