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NM_000135.4(FANCA):c.3349A>G (p.Arg1117Gly)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jul 30, 2021)
Last evaluated:
Jun 21, 2021
Accession:
VCV000219752.8
Variation ID:
219752
Description:
single nucleotide variant
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NM_000135.4(FANCA):c.3349A>G (p.Arg1117Gly)

Allele ID
222542
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 89746890 (GRCh38) GRCh38 UCSC
16: 89813298 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
O15360:p.Arg1117Gly
LRG_495t1:c.3349A>G
LRG_495:g.74768A>G
... more HGVS
Protein change
R1117G
Other names
-
Canonical SPDI
NC_000016.10:89746889:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA350699
UniProtKB: O15360#VAR_009651
dbSNP: rs149277003
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Jul 17, 2017 RCV000206698.4
Pathogenic 1 criteria provided, single submitter Mar 21, 2016 RCV000254722.1
Pathogenic 4 criteria provided, single submitter Jun 21, 2021 RCV000665865.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FANCA - - GRCh38
GRCh37
2154 2635

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 17, 2017)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia
Allele origin: germline
Invitae
Accession: SCV000259800.4
Submitted: (Oct 05, 2017)
Evidence details
Comment:
This sequence change replaces arginine with glycine at codon 1117 of the FANCA protein (p.Arg1117Gly). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(Mar 21, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000322263.7
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R1117G variant in the FANCA gene has been reported previously in association with Fanconi anemia when in trans with another disease-causing variant (Levran et … (more)
Pathogenic
(Jun 21, 2021)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia, complementation group A
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV001762383.1
Submitted: (Jul 30, 2021)
Evidence details
Publications
PubMed (7)
Comment:
FANCA c.3349A>G has been identified in multiple individuals with Fanconi anemia. This FANCA variant (rs149277003) is rare (<0.1%) in a large population dataset (gnomAD: 6/193422 … (more)
Likely pathogenic
(Mar 14, 2017)
no assertion criteria provided
Method: clinical testing
Fanconi anemia, complementation group A
Allele origin: unknown
Counsyl
Accession: SCV000790056.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (5)
Pathogenic
(Feb 28, 2020)
no assertion criteria provided
Method: curation
Fanconi anemia, complementation group A
Allele origin: germline
Leiden Open Variation Database
Accession: SCV001426115.1
Submitted: (Mar 04, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Curator: Arleen D. Auerbach. Submitters to LOVD: Arleen D. Auerbach, Johan de Winter, Sue Richards.
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Fanconi anemia, group A
Allele origin: germline
Natera, Inc.
Accession: SCV001462880.1
Submitted: (Dec 28, 2020)
Evidence details

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
FANCA Promotes DNA Double-Strand Break Repair by Catalyzing Single-Strand Annealing and Strand Exchange. Benitez A Molecular cell 2018 PMID: 30057198
A comprehensive approach to identification of pathogenic FANCA variants in Fanconi anemia patients and their families. Kimble DC Human mutation 2018 PMID: 29098742
Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification and PCR-Based Sanger Sequencing. Gille JJ Anemia 2012 PMID: 22778927
Validation of Fanconi anemia complementation Group A assignment using molecular analysis. Moghrabi NN Genetics in medicine : official journal of the American College of Medical Genetics 2009 PMID: 19367192
A rapid method for retrovirus-mediated identification of complementation groups in Fanconi anemia patients. Chandra S Molecular therapy : the journal of the American Society of Gene Therapy 2005 PMID: 16084127
A cytoplasmic serine protein kinase binds and may regulate the Fanconi anemia protein FANCA. Yagasaki H Blood 2001 PMID: 11739169
The fanconi anemia proteins FANCA and FANCG stabilize each other and promote the nuclear accumulation of the Fanconi anemia complex. Garcia-Higuera I Blood 2000 PMID: 11050007
Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Garcia-Higuera I Molecular and cellular biology 1999 PMID: 10373536
Sequence variation in the Fanconi anemia gene FAA. Levran O Proceedings of the National Academy of Sciences of the United States of America 1997 PMID: 9371798
Sequence variation in the Fanconi anemia gene FAA. Levran O Proceedings of the National Academy of Sciences of the United States of America 1997 PMID: 09371798

Text-mined citations for rs149277003...

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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 Sep 06, 2021