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NM_001018115.3(FANCD2):c.1684C>T (p.Gln562Ter) AND Fanconi anemia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 6, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003523184.1

Allele description [Variation Report for NM_001018115.3(FANCD2):c.1684C>T (p.Gln562Ter)]

NM_001018115.3(FANCD2):c.1684C>T (p.Gln562Ter)

Genes:
LOC107303338:3p25 FANCD2 Alu-mediated recombination region [Gene]
FANCD2:FA complementation group D2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_001018115.3(FANCD2):c.1684C>T (p.Gln562Ter)
HGVS:
  • NC_000003.12:g.10060321C>T
  • NG_007311.1:g.38893C>T
  • NG_046754.1:g.29475C>T
  • NM_001018115.3:c.1684C>TMANE SELECT
  • NM_001319984.2:c.1684C>T
  • NM_001374253.1:c.1573C>T
  • NM_001374254.1:c.1684C>T
  • NM_033084.6:c.1684C>T
  • NP_001018125.1:p.Gln562Ter
  • NP_001018125.1:p.Gln562Ter
  • NP_001306913.1:p.Gln562Ter
  • NP_001361182.1:p.Gln525Ter
  • NP_001361183.1:p.Gln562Ter
  • NP_149075.2:p.Gln562Ter
  • NP_149075.2:p.Gln562Ter
  • LRG_306t1:c.1684C>T
  • LRG_306t2:c.1684C>T
  • LRG_306:g.38893C>T
  • LRG_306p1:p.Gln562Ter
  • LRG_306p2:p.Gln562Ter
  • NC_000003.11:g.10102005C>T
  • NM_001018115.1:c.1684C>T
  • NM_033084.3:c.1684C>T
Protein change:
Q525*
Molecular consequence:
  • NM_001018115.3:c.1684C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001319984.2:c.1684C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374253.1:c.1573C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374254.1:c.1684C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_033084.6:c.1684C>T - nonsense - [Sequence Ontology: SO:0001587]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004344050Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 6, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Hypomorphic mutations in the gene encoding a key Fanconi anemia protein, FANCD2, sustain a significant group of FA-D2 patients with severe phenotype.

Kalb R, Neveling K, Hoehn H, Schneider H, Linka Y, Batish SD, Hunt C, Berwick M, Callen E, Surralles J, Casado JA, Bueren J, Dasi A, Soulier J, Gluckman E, Zwaan CM, van Spaendonk R, Pals G, de Winter JP, Joenje H, Grompe M, Auerbach AD, et al.

Am J Hum Genet. 2007 May;80(5):895-910. Epub 2007 Apr 6. Erratum in: Am J Hum Genet. 2007 Jul;81(1):196.

PubMed [citation]
PMID:
17436244
PMCID:
PMC1852747

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. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004344050.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Gln562*) in the FANCD2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCD2 are known to be pathogenic (PMID: 17436244). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FANCD2-related conditions. 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: Jun 17, 2024