ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.811C>T (p.Gln271Ter)

gnomAD frequency: 0.00001  dbSNP: rs372163487
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410151 SCV000486568 likely pathogenic Fanconi anemia complementation group A 2016-06-24 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001223227 SCV001395366 pathogenic Fanconi anemia 2024-09-10 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln271*) in the FANCA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCA are known to be pathogenic (PMID: 19367192). This variant is present in population databases (rs372163487, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with Fanconi anemia (PMID: 15643609, 16084127, 21659346, 29098742). ClinVar contains an entry for this variant (Variation ID: 371093). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Mayo Clinic Laboratories, Mayo Clinic RCV001509537 SCV001716293 pathogenic not provided 2019-07-26 criteria provided, single submitter clinical testing PVS1, PM2, PP5
GeneDx RCV001509537 SCV001757863 pathogenic not provided 2022-05-23 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 15643609, 29098742, 25111073, 16084127, 21659346)
Fulgent Genetics, Fulgent Genetics RCV000410151 SCV002813964 pathogenic Fanconi anemia complementation group A 2024-01-18 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV000410151 SCV004048427 pathogenic Fanconi anemia complementation group A criteria provided, single submitter clinical testing The stop gained variant c.811C>T (p.Gln271Ter) in FANCA gene has been reported previously in patients affected with Fanconi anemia (Chandra et al., 2005; Levran et al., 2005). The p.Pro790GlnfsTer98 variant is reported with the allele frequency (0.001%) in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. It has been submitted to ClinVar with varying interpretations: Pathogenic/Likely Pathogenic. The nucleotide change in FANCA is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss-offunction variants in FANCA are known to be pathogenic (Moghrabi et al., 2009). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000410151 SCV004196569 pathogenic Fanconi anemia complementation group A 2023-03-21 criteria provided, single submitter clinical testing
Leiden Open Variation Database RCV000410151 SCV001425777 pathogenic Fanconi anemia complementation group A 2020-02-28 no assertion criteria provided curation Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

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