NM_017547.4(FOXRED1):c.538C>T (p.Gln180Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 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:: RCV002926927.3

Allele description [Variation Report for NM_017547.4(FOXRED1):c.538C>T (p.Gln180Ter)]

NM_017547.4(FOXRED1):c.538C>T (p.Gln180Ter)

Gene:

FOXRED1:FAD dependent oxidoreductase domain containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q24.2

Genomic location:

Preferred name:

NM_017547.4(FOXRED1):c.538C>T (p.Gln180Ter)

HGVS:

NC_000011.10:g.126274928C>T
NG_028029.1:g.10889C>T
NM_017547.4:c.538C>TMANE SELECT
NP_060017.1:p.Gln180Ter
NC_000011.9:g.126144823C>T
NR_037647.2:n.370C>T
NR_037648.2:n.715C>T

Protein change:

Q180*

Molecular consequence:

NR_037647.2:n.370C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_037648.2:n.715C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_017547.4:c.538C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003255579	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 13, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20818383, 20858599, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003255579

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 13, 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

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency.

Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA, Redman MC, Wiltshire E, Wilson CJ, Altshuler D, Gabriel SB, Daly MJ, Thorburn DR, Mootha VK.

Nat Genet. 2010 Oct;42(10):851-8. doi: 10.1038/ng.659. Epub 2010 Sep 5.

PubMed [citation]

PMID:: 20818383
PMCID:: PMC2977978

FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy.

Fassone E, Duncan AJ, Taanman JW, Pagnamenta AT, Sadowski MI, Holand T, Qasim W, Rutland P, Calvo SE, Mootha VK, Bitner-Glindzicz M, Rahman S.

Hum Mol Genet. 2010 Dec 15;19(24):4837-47. doi: 10.1093/hmg/ddq414. Epub 2010 Sep 21. Erratum in: Hum Mol Genet. 2015 Jul 15;24(14):4183. doi: 10.1093/hmg/ddv164.

PubMed [citation]

PMID:: 20858599
PMCID:: PMC4560042

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003255579.2

#	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.Gln180*) in the FOXRED1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FOXRED1 are known to be pathogenic (PMID: 20818383, 20858599). This variant is present in population databases (rs760964794, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with FOXRED1-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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: Sep 29, 2024

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