NM_000136.3(FANCC):c.487_490del (p.Glu163fs) AND Fanconi anemia, complementation group C

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Dec 15, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000410607.6

Allele description [Variation Report for NM_000136.3(FANCC):c.487_490del (p.Glu163fs)]

NM_000136.3(FANCC):c.487_490del (p.Glu163fs)

Gene:
FANCC:FA complementation group C [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000136.3(FANCC):c.487_490del (p.Glu163fs)
HGVS:
  • NC_000009.11:g.97933392_97933395del
  • NC_000009.12:g.95171111CT[1]
  • NG_011707.1:g.151595GA[1]
  • NM_000136.3:c.487_490delMANE SELECT
  • NM_001243743.2:c.487_490del
  • NM_001243744.2:c.487_490del
  • NP_000127.2:p.Glu163fs
  • NP_001230672.1:p.Glu163fs
  • NP_001230673.1:p.Glu163fs
  • LRG_497t1:c.487_490del
  • LRG_497:g.151595GA[1]
  • NC_000009.11:g.97933392_97933395del
  • NC_000009.11:g.97933393CT[1]
  • NC_000009.11:g.97933395_97933398delCTCT
  • NM_000136.2:c.487_490del
  • NM_000136.2:c.487_490delGAGA
  • NM_000136.3:c.487_490delGAGAMANE SELECT
  • p.E163IfsX30
Protein change:
E163fs
Links:
dbSNP: rs730881708
NCBI 1000 Genomes Browser:
rs730881708
Molecular consequence:
  • NM_000136.3:c.487_490del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001243743.2:c.487_490del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001243744.2:c.487_490del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Fanconi anemia, complementation group C (FANCC)
Synonyms:
FANCONI PANCYTOPENIA, TYPE 3; FACC; Fanconi anemia, group C
Identifiers:
MONDO: MONDO:0009213; MedGen: C3468041; Orphanet: 84; OMIM: 227645

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000486096Counsylno assertion criteria providedLikely pathogenic
(Dec 28, 2017)
unknownclinical testing

SCV000695433Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(Oct 9, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV001163626Baylor Geneticscriteria provided, single submitter
Pathogenicgermlineclinical testing

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

SCV001365297Leiden Open Variation Databaseno assertion criteria providedPathogenic
(Feb 28, 2020)
germlinecuration

SCV001478122Department of Pediatrics,Memorial Sloan Kettering Cancer Centercriteria provided, single submitter
Pathogenic
(Dec 15, 2020)
germlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedresearch
not providedgermlineyesnot providednot providednot providednot providednot providedcuration
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing.

Susswein LR, Marshall ML, Nusbaum R, Vogel Postula KJ, Weissman SM, Yackowski L, Vaccari EM, Bissonnette J, Booker JK, Cremona ML, Gibellini F, Murphy PD, Pineda-Alvarez DE, Pollevick GD, Xu Z, Richard G, Bale S, Klein RT, Hruska KS, Chung WK.

Genet Med. 2016 Aug;18(8):823-32. doi: 10.1038/gim.2015.166. Epub 2015 Dec 17. Erratum in: Genet Med. 2016 May;18(5):531-2.

PubMed [citation]
PMID:
26681312
PMCID:
PMC4985612

Association Between Inherited Germline Mutations in Cancer Predisposition Genes and Risk of Pancreatic Cancer.

Hu C, Hart SN, Polley EC, Gnanaolivu R, Shimelis H, Lee KY, Lilyquist J, Na J, Moore R, Antwi SO, Bamlet WR, Chaffee KG, DiCarlo J, Wu Z, Samara R, Kasi PM, McWilliams RR, Petersen GM, Couch FJ.

JAMA. 2018 Jun 19;319(23):2401-2409. doi: 10.1001/jama.2018.6228.

PubMed [citation]
PMID:
29922827
PMCID:
PMC6092184
See all PubMed Citations (5)

Details of each submission

From Counsyl, SCV000486096.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695433.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: FANCC c.487_490delGAGA (p.Glu163IlefsX30) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 2.4e-05 in 251214 control chromosomes. c.487_490delGAGA has been reported in the literature in an individual affected with ovarian cancer (Susswein_2015). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

From Baylor Genetics, SCV001163626.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Leiden Open Variation Database, SCV001365297.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

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

From Department of Pediatrics,Memorial Sloan Kettering Cancer Center, SCV001478122.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 6, 2021

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