NM_000136.3(FANCC):c.1199del (p.Phe400fs) AND Fanconi anemia

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 7, 2020
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:: RCV001381279.4

Allele description

NM_000136.3(FANCC):c.1199del (p.Phe400fs)

Genes:

FANCC:FA complementation group C [Gene - OMIM - HGNC]
AOPEP:aminopeptidase O (putative) [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000136.3(FANCC):c.1199del (p.Phe400fs)

HGVS:

NC_000009.12:g.95111594del
NG_011707.1:g.211117del
NM_000136.3:c.1199delMANE SELECT
NM_001243743.2:c.1199del
NM_001243744.2:c.1199del
NP_000127.2:p.Phe400fs
NP_001230672.1:p.Phe400fs
NP_001230673.1:p.Phe400fs
LRG_497:g.211117del
NC_000009.11:g.97873875del
NC_000009.11:g.97873876del

Protein change:

F400fs

Links:

dbSNP: rs2134550787

NCBI 1000 Genomes Browser:

rs2134550787

Molecular consequence:

NM_000136.3:c.1199del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243743.2:c.1199del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243744.2:c.1199del - 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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RNA for Nucleotide (Select 294489305) (17)
Nucleotide
Bacillus oceanisediminis strain p83_H06 16S ribosomal RNA gene, partial sequence
Bacillus oceanisediminis strain p83_H06 16S ribosomal RNA gene, partial sequence
gi|388833787|gb|JQ834943.1|

Nucleotide
Bacillus arbutinivorans strain p83_H09 16S ribosomal RNA gene, partial sequence
Bacillus arbutinivorans strain p83_H09 16S ribosomal RNA gene, partial sequence
gi|388833790|gb|JQ834946.1|

Nucleotide
Bacillus cereus strain p83_H01 16S ribosomal RNA gene, partial sequence
Bacillus cereus strain p83_H01 16S ribosomal RNA gene, partial sequence
gi|388833783|gb|JQ834939.1|

Nucleotide
Bacillus pumilus strain p83_G07 16S ribosomal RNA gene, partial sequence
Bacillus pumilus strain p83_G07 16S ribosomal RNA gene, partial sequence
gi|388833777|gb|JQ834933.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001579600	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 7, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17924555, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001579600

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 7, 2020)

germline

clinical testing

PubMed (2)
[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

Genetic subtyping of Fanconi anemia by comprehensive mutation screening.

Ameziane N, Errami A, Léveillé F, Fontaine C, de Vries Y, van Spaendonk RM, de Winter JP, Pals G, Joenje H.

Hum Mutat. 2008 Jan;29(1):159-66.

PubMed [citation]

PMID:: 17924555

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, SCV001579600.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in FANCC are known to be pathogenic (PMID: 17924555). This variant has not been reported in the literature in individuals with FANCC-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Phe400Serfs*13) in the FANCC gene. It is expected to result in an absent or disrupted protein product.

#	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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