NM_001113378.2(FANCI):c.3147del (p.Leu1049fs) AND Fanconi anemia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 25, 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:: RCV003779030.3

Allele description [Variation Report for NM_001113378.2(FANCI):c.3147del (p.Leu1049fs)]

NM_001113378.2(FANCI):c.3147del (p.Leu1049fs)

Gene:

FANCI:FA complementation group I [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q26.1

Genomic location:

Preferred name:

NM_001113378.2(FANCI):c.3147del (p.Leu1049fs)

HGVS:

NC_000015.10:g.89305203del
NG_008218.2:g.34593del
NG_011736.1:g.66241del
NG_160687.1:g.146del
NM_001113378.2:c.3147delMANE SELECT
NM_001376910.1:c.2868del
NM_001376911.1:c.3147del
NM_018193.3:c.2967del
NP_001106849.1:p.Leu1049Phefs
NP_001106849.1:p.Leu1049fs
NP_001363839.1:p.Leu956fs
NP_001363840.1:p.Leu1049fs
NP_060663.2:p.Leu989fs
LRG_500t1:c.3147del
LRG_500:g.66241del
LRG_500p1:p.Leu1049Phefs
LRG_765:g.34593del
NC_000015.9:g.89848434del
NM_001113378.1:c.3147delG

Protein change:

L1049fs

Molecular consequence:

NM_001113378.2:c.3147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001376910.1:c.2868del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001376911.1:c.3147del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_018193.3:c.2967del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004663022	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 25, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17452773, 17460694, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004663022

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 25, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

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

FANCI is a second monoubiquitinated member of the Fanconi anemia pathway.

Sims AE, Spiteri E, Sims RJ 3rd, Arita AG, Lach FP, Landers T, Wurm M, Freund M, Neveling K, Hanenberg H, Auerbach AD, Huang TT.

Nat Struct Mol Biol. 2007 Jun;14(6):564-7. Epub 2007 Apr 25.

PubMed [citation]

PMID:: 17460694

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004663022.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Leu1049Phefs*12) in the FANCI gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCI are known to be pathogenic (PMID: 17452773, 17460694). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FANCI-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 5, 2025

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