NM_022725.4(FANCF):c.267_268del (p.Cys89_Asp90delinsTer) AND Fanconi anemia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 13, 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:: RCV003636027.1

Allele description [Variation Report for NM_022725.4(FANCF):c.267_268del (p.Cys89_Asp90delinsTer)]

NM_022725.4(FANCF):c.267_268del (p.Cys89_Asp90delinsTer)

Gene:

FANCF:FA complementation group F [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11p14.3

Genomic location:

Preferred name:

NM_022725.4(FANCF):c.267_268del (p.Cys89_Asp90delinsTer)

HGVS:

NC_000011.10:g.22625543CA[1]
NG_007425.1:g.5296TG[1]
NG_122096.1:g.257CA[1]
NG_122096.2:g.331CA[1]
NM_022725.4:c.267_268delMANE SELECT
NP_073562.1:p.Cys89Terfs
NP_073562.1:p.Cys89_Asp90delinsTer
LRG_527t1:c.265_266TG[1]
LRG_527:g.5296TG[1]
LRG_527p1:p.Cys89Terfs
NC_000011.9:g.22647089CA[1]
NC_000011.9:g.22647089_22647090del
NM_022725.3:c.265_266TG[1]

Molecular consequence:

NM_022725.4:c.267_268del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004508640	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 13, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11063725, 12649160, 27714961, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004508640

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 13, 2023)

germline

clinical testing

PubMed (4)
[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

The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG.

de Winter JP, van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper RJ, Kruyt FA, Hoatlin ME, Joenje H.

Hum Mol Genet. 2000 Nov 1;9(18):2665-74.

PubMed [citation]

PMID:: 11063725

Fanconi anemia protein complex: mapping protein interactions in the yeast 2- and 3-hybrid systems.

Gordon SM, Buchwald M.

Blood. 2003 Jul 1;102(1):136-41. Epub 2003 Mar 20.

PubMed [citation]

PMID:: 12649160

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004508640.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant has not been reported in the literature in individuals affected with FANCF-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys89*) in the FANCF gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 286 amino acid(s) of the FANCF protein. This variant disrupts a region of the FANCF protein in which other variant(s) (p.Gly233Glufs*32) have been determined to be pathogenic (PMID: 11063725, 12649160, 27714961). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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: Feb 28, 2024

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