NM_000136.3(FANCC):c.37C>T (p.Gln13Ter) AND Fanconi anemia

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 24, 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:: RCV000476519.20

Allele description [Variation Report for NM_000136.3(FANCC):c.37C>T (p.Gln13Ter)]

NM_000136.3(FANCC):c.37C>T (p.Gln13Ter)

Gene:

FANCC:FA complementation group C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q22.32

Genomic location:

Preferred name:

NM_000136.3(FANCC):c.37C>T (p.Gln13Ter)

Other names:

p.Q13*:CAG>TAG

HGVS:

NC_000009.12:g.95249255G>A
NG_011707.1:g.73455C>T
NM_000136.3:c.37C>TMANE SELECT
NM_001243743.2:c.37C>T
NM_001243744.2:c.37C>T
NP_000127.2:p.Gln13Ter
NP_000127.2:p.Gln13Ter
NP_001230672.1:p.Gln13Ter
NP_001230673.1:p.Gln13Ter
NP_001230673.1:p.Gln13Ter
LRG_497t1:c.37C>T
LRG_497:g.73455C>T
LRG_497p1:p.Gln13Ter
NC_000009.11:g.98011537G>A
NM_000136.2:c.37C>T
NM_001243744.1:c.37C>T
c.37C>T (p.Gln13*)
p.Gln13Stop

Protein change:

Q13*; GLN13TER

Links:

OMIM: 613899.0004; dbSNP: rs121917784

NCBI 1000 Genomes Browser:

rs121917784

Molecular consequence:

NM_000136.3:c.37C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001243743.2:c.37C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001243744.2:c.37C>T - 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
SCV000549951	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 24, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 8103176, 8128956, 9207444, 26740942, 17924555, 28492532
SCV002081319	Natera, Inc.	no assertion criteria provided	Pathogenic (Mar 17, 2017)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000549951

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 24, 2023)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002081319

Natera, Inc.

no assertion criteria provided

Pathogenic
(Mar 17, 2017)

germline

clinical testing

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

FACC gene mutations and early prenatal diagnosis of Fanconi's anaemia.

Murer-Orlando M, Llerena JC Jr, Birjandi F, Gibson RA, Mathew CG.

Lancet. 1993 Sep 11;342(8872):686. No abstract available.

PubMed [citation]

PMID:: 8103176

Mutation analysis of the Fanconi anemia gene FACC.

Verlander PC, Lin JD, Udono MU, Zhang Q, Gibson RA, Mathew CG, Auerbach AD.

Am J Hum Genet. 1994 Apr;54(4):595-601.

PubMed [citation]

PMID:: 8128956
PMCID:: PMC1918103

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV000549951.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 12046). This variant is also known as c.292C>T. This premature translational stop signal has been observed in individual(s) with Fanconi anemia (PMID: 8103176, 8128956, 9207444, 26740942). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs121917784, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Gln13*) in the FANCC gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCC are known to be pathogenic (PMID: 17924555).

#	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

From Natera, Inc., SCV002081319.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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: Jun 17, 2024

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