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NM_001113378.2(FANCI):c.3853C>T (p.Arg1285Ter) AND Fanconi anemia complementation group I

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Mar 27, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000001024.12

Allele description [Variation Report for NM_001113378.2(FANCI):c.3853C>T (p.Arg1285Ter)]

NM_001113378.2(FANCI):c.3853C>T (p.Arg1285Ter)

Gene:
FANCI:FA complementation group I [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q26.1
Genomic location:
Preferred name:
NM_001113378.2(FANCI):c.3853C>T (p.Arg1285Ter)
Other names:
NM_001113378.1:c.3853C>T
HGVS:
  • NC_000015.10:g.89315318C>T
  • NG_008218.2:g.24478G>A
  • NG_011736.1:g.76356C>T
  • NM_001113378.2:c.3853C>TMANE SELECT
  • NM_001376910.1:c.3574C>T
  • NM_001376911.1:c.3853C>T
  • NM_018193.3:c.3673C>T
  • NP_001106849.1:p.Arg1285Ter
  • NP_001363839.1:p.Arg1192Ter
  • NP_001363840.1:p.Arg1285Ter
  • NP_060663.2:p.Arg1225Ter
  • LRG_500:g.76356C>T
  • LRG_765:g.24478G>A
  • NC_000015.9:g.89858549C>T
Protein change:
R1192*; ARG1285TER
Links:
OMIM: 611360.0003; dbSNP: rs121918164
NCBI 1000 Genomes Browser:
rs121918164
Molecular consequence:
  • NM_001113378.2:c.3853C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001376910.1:c.3574C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001376911.1:c.3853C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_018193.3:c.3673C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Fanconi anemia complementation group I (FANCI)
Identifiers:
MONDO: MONDO:0012186; MedGen: C1836861; Orphanet: 84; OMIM: 609053

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000021174OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 2007)
germlineliterature only

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

SCV001364861Leiden Open Variation Database
no assertion criteria provided
Pathogenic
(Feb 7, 2011)
germlinecuration

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

SCV004047489Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

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

SCV004199188Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 27, 2024)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, curation
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Identification of the Fanconi anemia complementation group I gene, FANCI.

Dorsman JC, Levitus M, Rockx D, Rooimans MA, Oostra AB, Haitjema A, Bakker ST, Steltenpool J, Schuler D, Mohan S, Schindler D, Arwert F, Pals G, Mathew CG, Waisfisz Q, de Winter JP, Joenje H.

Cell Oncol. 2007;29(3):211-8.

PubMed [citation]
PMID:
17452773
PMCID:
PMC4618213

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV000021174.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a male Hungarian child with Fanconi anemia complementation group I (FANCI; 609053) who had nonconsanguineous parents, Dorsman et al. (2007) identified compound heterozygosity for mutations in the FANCI gene. The mutation on the maternal allele was a C-to-T transition at nucleotide 3853 in exon 37 of the FANCI cDNA, resulting in an arg1285-to-ter (R964X) substitution. The mutation on the paternal allele was an A-to-G transition at nucleotide -88 in intron 31 (3350-88A-G using the cDNA numbering; 611360.0004), which created a novel splice donor site and resulted in an additional exon. The patient died at age 12 years.

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

From Leiden Open Variation Database, SCV001364861.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

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 Neuberg Centre For Genomic Medicine, NCGM, SCV004047489.1

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

Description

The stop gained variant c.3853C>T (p.Arg1285Ter) in FANCI has been reported previously in heterozygous state in patients affected with individuals with Fanconi anemia (Dorsman et al.). The p.Arg1285Ter variant has allele frequency in gnomAD exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. The observed variant is not detected in the spouse.

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

From Baylor Genetics, SCV004199188.2

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

Last Updated: Jun 17, 2024