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NM_144997.7(FLCN):c.1300+2T>A AND Birt-Hogg-Dube syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 2, 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:
RCV003607840.1

Allele description

NM_144997.7(FLCN):c.1300+2T>A

Gene:
FLCN:folliculin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p11.2
Genomic location:
Preferred name:
NM_144997.7(FLCN):c.1300+2T>A
HGVS:
  • NC_000017.11:g.17216378A>T
  • NG_008001.2:g.25811T>A
  • NM_001353229.2:c.1354+2T>A
  • NM_001353230.2:c.1300+2T>A
  • NM_001353231.2:c.1300+2T>A
  • NM_144997.7:c.1300+2T>AMANE SELECT
  • LRG_325:g.25811T>A
  • NC_000017.10:g.17119692A>T
Molecular consequence:
  • NM_001353229.2:c.1354+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353230.2:c.1300+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353231.2:c.1300+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_144997.7:c.1300+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Birt-Hogg-Dube syndrome
Synonyms:
BHD syndrome; Birt Hogg Dubé syndrome
Identifiers:
MONDO: MONDO:0800444; MedGen: C0346010; Orphanet: 122; OMIM: PS135150

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004410761Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Nov 2, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Constitutional FLCN mutations in patients with suspected Birt-Hogg-Dubé syndrome ascertained for non-cutaneous manifestations.

Maffé A, Toschi B, Circo G, Giachino D, Giglio S, Rizzo A, Carloni A, Poletti V, Tomassetti S, Ginardi C, Ungari S, Genuardi M.

Clin Genet. 2011 Apr;79(4):345-54. doi: 10.1111/j.1399-0004.2010.01480.x.

PubMed [citation]
PMID:
20618353

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004410761.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individual(s) with Birt-Hogg-Dubé syndrome (PMID: 20618353). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 11 of the FLCN gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in FLCN are known to be pathogenic (PMID: 15852235).

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

Last Updated: Jun 9, 2024