NM_000135.4(FANCA):c.2853-15_2856del AND Fanconi anemia

Clinical significance:Pathogenic (Last evaluated: Jul 3, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001384022.1

Allele description [Variation Report for NM_000135.4(FANCA):c.2853-15_2856del]

NM_000135.4(FANCA):c.2853-15_2856del

Gene:
FANCA:FA complementation group A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000135.4(FANCA):c.2853-15_2856del
HGVS:
  • NC_000016.10:g.89758706_89758724del
  • NG_011706.1:g.62938_62956del
  • NM_000135.4:c.2853-15_2856delMANE SELECT
  • NM_001286167.3:c.2853-15_2856del
  • LRG_495t1:c.2853-15_2856del
  • LRG_495:g.62938_62956del
  • NC_000016.9:g.89825110_89825128del
  • NC_000016.9:g.89825114_89825132del
  • NM_000135.2:c.2853-15_2856del
  • NM_000135.2:c.2853-15_2856del19
Links:
dbSNP: rs1285346388
NCBI 1000 Genomes Browser:
rs1285346388
Molecular consequence:
  • NM_000135.4:c.2853-15_2856del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001286167.3:c.2853-15_2856del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Fanconi anemia (FA)
Synonyms:
Fanconi pancytopenia; Fanconi's anemia
Identifiers:
MONDO: MONDO:0019391; MeSH: D005199; MedGen: C0015625; Orphanet: 84; OMIM: PS227650

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001583384Invitaecriteria provided, single submitter
Pathogenic
(Jul 3, 2020)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sequence variation in the Fanconi anemia gene FAA.

Levran O, Erlich T, Magdalena N, Gregory JJ, Batish SD, Verlander PC, Auerbach AD.

Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):13051-6.

PubMed [citation]
PMID:
9371798
PMCID:
PMC24261

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, Bottega R, Cappelli E, Cavani S, Criscuolo M, Nicchia E, Corsolini F, Greco C, Borriello A, Svahn J, Pillon M, Mecucci C, Casazza G, Verzegnassi F, Cugno C, Locasciulli A, Farruggia P, Longoni D, Ramenghi U, Barberi W, Tucci F, Perrotta S, et al.

Haematologica. 2014 Jun;99(6):1022-31. doi: 10.3324/haematol.2014.104224. Epub 2014 Feb 28. Erratum in: Haematologica. 2014 Sep;99(9):1532.

PubMed [citation]
PMID:
24584348
PMCID:
PMC4040906
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV001583384.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This variant results in the deletion of part of exon 30 (c.2853-15_2856del) of the FANCA gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with Fanconi anemia (PMID: 17924555, 9371798). This variant is also known as c.2853-19del19 or IVS29(-19)-1del. ClinVar contains an entry for this variant (Variation ID: 550055). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant disrupts the p.Arg951 amino acid residue in FANCA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24584348, 24349332, 17924555, 26799702). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Loss-of-function variants in FANCA are known to be pathogenic (PMID: 19367192). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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