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NM_144997.7(FLCN):c.1580G>A (p.Arg527Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Feb 10, 2021)
Last evaluated:
Aug 26, 2020
Accession:
VCV000460603.8
Variation ID:
460603
Description:
single nucleotide variant
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NM_144997.7(FLCN):c.1580G>A (p.Arg527Gln)

Allele ID
467111
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17p11.2
Genomic location
17: 17213815 (GRCh38) GRCh38 UCSC
17: 17117129 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_325t1:c.1580G>A
LRG_325:g.28374G>A
NC_000017.10:g.17117129C>T
... more HGVS
Protein change
R527Q, R545Q
Other names
-
Canonical SPDI
NC_000017.11:17213814:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00004
Links
ClinGen: CA8415934
dbSNP: rs777826268
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jun 20, 2018 RCV000565191.1
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001121961.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Aug 26, 2020 RCV000560552.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FLCN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1159 1275

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 26, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: germline
Invitae
Accession: SCV000632854.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces arginine with glutamine at codon 527 of the FLCN protein (p.Arg527Gln). The arginine residue is highly conserved and there is a … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001280627.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Pneumothorax, primary spontaneous
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001280628.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jun 20, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000673425.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The p.R527Q variant (also known as c.1580G>A), located in coding exon 11 of the FLCN gene, results from a G to A substitution at nucleotide … (more)
Uncertain significance
(Sep 10, 2019)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: unknown
Baylor Genetics
Study: CSER-TexasKidsCanSeq
Accession: SCV001481573.2
Submitted: (Feb 10, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs777826268...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021