ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.4015del (p.Leu1339fs)

gnomAD frequency: 0.00003  dbSNP: rs762902309
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Individualized Medicine, Mayo Clinic RCV000190642 SCV000245685 likely pathogenic Fanconi anemia complementation group A 2014-01-01 criteria provided, single submitter research
Counsyl RCV000190642 SCV000486569 likely pathogenic Fanconi anemia complementation group A 2016-11-02 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001043860 SCV001207627 pathogenic Fanconi anemia 2024-12-23 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu1339Serfs*24) 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 not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Fanconi anemia or breast cancer (PMID: 10521298, 26296701, 29098742). ClinVar contains an entry for this variant (Variation ID: 208638). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000190642 SCV002022311 pathogenic Fanconi anemia complementation group A 2020-10-09 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000190642 SCV002811195 pathogenic Fanconi anemia complementation group A 2024-01-23 criteria provided, single submitter clinical testing
GeneDx RCV003325465 SCV004032021 pathogenic not provided 2024-01-23 criteria provided, single submitter clinical testing Observed with a second variant in unrelated patients with Fanconi anemia in the published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (PMID: 10521298, 29098742); Reported in the heterozygous state in an individual with breast cancer who tested negative for pathogenic variants in the BRCA1 and BRCA2 genes (PMID: 26296701); Frameshift 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 significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 33084842, 10521298, 29098742, 19367192, 26296701)
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV000190642 SCV004171432 pathogenic Fanconi anemia complementation group A 2023-11-28 criteria provided, single submitter clinical testing The FANCA c.4015del (p.Leu1339SerfsTer24) change deletes one nucleotide to cause a frameshift and the creation of a premature stop codon. This change is predicted to cause protein truncation or absence of protein due to nonsense-mediated decay. This variant has been reported in individuals with Fanconi anemia (PMID: 10521298, 29098742). This variant is absent in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as pathogenic.
Baylor Genetics RCV000190642 SCV004196045 pathogenic Fanconi anemia complementation group A 2023-08-29 criteria provided, single submitter clinical testing
Leiden Open Variation Database RCV000190642 SCV001425727 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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