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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 3, 2024
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:: RCV005090932.1

Allele description [Variation Report for NM_144997.7(FLCN):c.1300+2T>G]

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

HGVS:

NC_000017.11:g.17216378A>C
NG_008001.2:g.25811T>G
NM_001353229.2:c.1354+2T>G
NM_001353230.2:c.1300+2T>G
NM_001353231.2:c.1300+2T>G
NM_144997.7:c.1300+2T>GMANE SELECT
LRG_325t1:c.1300+2T>G
LRG_325:g.25811T>G
NC_000017.10:g.17119692A>C
NM_144997.5:c.1300+2T>G

Links:

dbSNP: rs1064793766

NCBI 1000 Genomes Browser:

rs1064793766

Molecular consequence:

NM_001353229.2:c.1354+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353230.2:c.1300+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353231.2:c.1300+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_144997.7:c.1300+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005765944	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Sep 3, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16199547, 15852235, 20618353, 37490463, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005765944

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Sep 3, 2024)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

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

Germline BHD-mutation spectrum and phenotype analysis of a large cohort of families with Birt-Hogg-Dubé syndrome.

Schmidt LS, Nickerson ML, Warren MB, Glenn GM, Toro JR, Merino MJ, Turner ML, Choyke PL, Sharma N, Peterson J, Morrison P, Maher ER, Walther MM, Zbar B, Linehan WM.

Am J Hum Genet. 2005 Jun;76(6):1023-33. Epub 2005 Apr 25.

PubMed [citation]

PMID:: 15852235
PMCID:: PMC1196440

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005765944.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

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). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with clinical features of Birt‚ÄìHogg‚ÄìDube ÃÅ syndrome (PMID: 20618353, 37490463). ClinVar contains an entry for this variant (Variation ID: 419280). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

#	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: May 16, 2025

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