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NM_000135.4(FANCA):c.2852G>A (p.Arg951Gln)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Oct 4, 2021)
Last evaluated:
Sep 1, 2021
Accession:
VCV000526433.13
Variation ID:
526433
Description:
single nucleotide variant
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NM_000135.4(FANCA):c.2852G>A (p.Arg951Gln)

Allele ID
530933
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 89761949 (GRCh38) GRCh38 UCSC
16: 89828357 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.9:g.89828357C>T
NC_000016.10:g.89761949C>T
NG_011706.1:g.59709G>A
... more HGVS
Protein change
R951Q
Other names
-
Canonical SPDI
NC_000016.10:89761948:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00005
Trans-Omics for Precision Medicine (TOPMed) 0.00009
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD), exomes 0.00005
Links
ClinGen: CA8251481
dbSNP: rs755922289
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, multiple submitters, no conflicts Sep 1, 2021 RCV001569733.6
Likely pathogenic 3 criteria provided, single submitter Apr 24, 2017 RCV000666705.3
Pathogenic 1 criteria provided, single submitter Oct 28, 2020 RCV000630961.4
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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
2162 2653

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Apr 24, 2017)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia, complementation group A
Allele origin: unknown
Counsyl
Accession: SCV000791048.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (6)
Pathogenic
(Oct 28, 2020)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia
Allele origin: germline
Invitae
Accession: SCV000751937.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (8)
Comment:
This sequence change replaces arginine with glutamine at codon 951 of the FANCA protein (p.Arg951Gln). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(Apr 14, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001793868.1
Submitted: (Aug 19, 2021)
Evidence details
Comment:
Published functional studies demonstrate a damaging effect: retention in the cytoplasm preventing cells from repairing DNA (Bottega et al,. 2018); In silico analysis supports that … (more)
Pathogenic
(Sep 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001961640.1
Submitted: (Oct 04, 2021)
Evidence details
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Fanconi anemia, group A
Allele origin: germline
Natera, Inc.
Accession: SCV001452857.1
Submitted: (Dec 28, 2020)
Evidence details
Pathogenic
(Jun 01, 2021)
no assertion criteria provided
Method: literature only
Fanconi anemia, complementation group A
Allele origin: germline
GeneReviews
Accession: SCV001737414.1
Submitted: (Jun 08, 2021)
Evidence details
Publications
PubMed (2)
BookShelf: NBK1401
Comment:
Associated with slower hematologic disease progression
Likely pathogenic
(-)
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: SCV001809681.1
Submitted: (Aug 24, 2021)
Evidence details
Pathogenic
(-)
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: SCV001959168.1
Submitted: (Sep 30, 2021)
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
Fanconi Anemia Mehta PA - 2021 PMID: 20301575
Hypomorphic FANCA mutations correlate with mild mitochondrial and clinical phenotype in Fanconi anemia. Bottega R Haematologica 2018 PMID: 29269525
FANCA Gene Mutations with 8 Novel Molecular Changes in Indian Fanconi Anemia Patients. Solanki A PloS one 2016 PMID: 26799702
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Molecular analysis of Fanconi anemia: the experience of the Bone Marrow Failure Study Group of the Italian Association of Pediatric Onco-Hematology. De Rocco D Haematologica 2014 PMID: 24584348
Human Fanconi anemia complementation group a protein stimulates the 5' flap endonuclease activity of FEN1. Qian L PloS one 2013 PMID: 24349332
Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification and PCR-Based Sanger Sequencing. Gille JJ Anemia 2012 PMID: 22778927
Genetic subtyping of Fanconi anemia by comprehensive mutation screening. Ameziane N Human mutation 2008 PMID: 17924555
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Reverse mosaicism in Fanconi anemia: natural gene therapy via molecular self-correction. Gross M Cytogenetic and genome research 2002 PMID: 12697994
The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG. de Winter JP Human molecular genetics 2000 PMID: 11063725
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs755922289...

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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