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NM_144997.7(FLCN):c.959G>A (p.Arg320Gln)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 30, 2021)
Last evaluated:
Aug 19, 2021
Accession:
VCV000041863.10
Variation ID:
41863
Description:
single nucleotide variant
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NM_144997.7(FLCN):c.959G>A (p.Arg320Gln)

Allele ID
50302
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17p11.2
Genomic location
17: 17219122 (GRCh38) GRCh38 UCSC
17: 17122436 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q8NFG4:p.Arg320Gln
LRG_325t1:c.959G>A
LRG_325:g.23067G>A
... more HGVS
Protein change
R320Q, R338Q
Other names
-
Canonical SPDI
NC_000017.11:17219121:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00067
Trans-Omics for Precision Medicine (TOPMed) 0.00072
Exome Aggregation Consortium (ExAC) 0.00078
The Genome Aggregation Database (gnomAD), exomes 0.00081
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00115
Links
ClinGen: CA159801
UniProtKB: Q8NFG4#VAR_025358
dbSNP: rs143483053
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000226709.8
Likely benign 4 criteria provided, single submitter Aug 19, 2021 RCV000034797.6
Likely benign 1 criteria provided, single submitter Dec 26, 2018 RCV000163434.4
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000374324.2
not provided 1 no assertion provided Sep 19, 2013 RCV000121114.3
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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
Likely benign
(Dec 26, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213980.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Does not segregate with disease in family study (genes with incomplete penetrance);In silico models in agreement (benign);Other data supporting benign classification
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: germline
Invitae
Accession: SCV000291455.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000401005.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (3)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Pneumothorax, primary spontaneous
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000401004.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Aug 19, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000724487.1
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28873162, 24728327, 22703879, 14627671, 27146957, 20522427, 21794948)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001809541.1
Submitted: (Aug 24, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001953426.1
Submitted: (Sep 30, 2021)
Evidence details
variant of unknown significance
(Jul 13, 2012)
no assertion criteria provided
Method: research
not provided
Allele origin: germline
Biesecker Lab/Clinical Genomics Section,National Institutes of Health
Study: ClinSeq
Accession: SCV000043265.1
Submitted: (Jul 15, 2012)
Evidence details
Publications
PubMed (1)
Comment:
Converted during submission to Uncertain significance.
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085282.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

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
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327
Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Johnston JJ American journal of human genetics 2012 PMID: 22703879
Analysis of the Birt-Hogg-Dubé (BHD) tumour suppressor gene in sporadic renal cell carcinoma and colorectal cancer. da Silva NF Journal of medical genetics 2003 PMID: 14627671

Text-mined citations for rs143483053...

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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 Oct 02, 2021