NM_000135.2(FANCA):c.238delT (p.Cys80Valfs) AND Fanconi anemia

Clinical significance:Pathogenic (Last evaluated: Jul 28, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000204795.1

Allele description [Variation Report for NM_000135.2(FANCA):c.238delT (p.Cys80Valfs)]

NM_000135.2(FANCA):c.238delT (p.Cys80Valfs)

Gene:
FANCA:FA complementation group A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000135.2(FANCA):c.238delT (p.Cys80Valfs)
HGVS:
  • NC_000016.10:g.89814565delA
  • NG_011706.1:g.7093delT
  • NM_000135.2:c.238delT
  • NP_000126.2:p.Cys80Valfs
  • LRG_495t1:c.238delT
  • LRG_495:g.7093delT
  • LRG_495p1:p.Cys80Valfs
  • NC_000016.9:g.89880973delA
Links:
dbSNP: rs864622187
NCBI 1000 Genomes Browser:
rs864622187
Molecular consequence:
  • NM_000135.2:c.238delT - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Fanconi anemia (FA)
Synonyms:
Fanconi's anemia
Identifiers:
MedGen: C0015625; OMIM: PS227650

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000259616Invitaecriteria provided, single submitter
Pathogenic
(Jul 28, 2015)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000259616.2

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

Description

This sequence change deletes 1 nucleotide from exon 3 of the FANCA mRNA (c.238delT), causing a frameshift at codon 80. This creates a premature translational stop signal (p.Cys80Valfs*15) and is expected to result in an absent or disrupted protein product. Truncating variants in FANCA are known to be pathogenic. This particular truncation has been reported as homozygous in a patient with Fanconia Anemia (PMID: 21273304). 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: Sep 14, 2018