NM_001278716.2(FBXL4):c.1751G>T (p.Cys584Phe) AND Mitochondrial DNA depletion syndrome 13

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 2017
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:: RCV000503096.1

Allele description [Variation Report for NM_001278716.2(FBXL4):c.1751G>T (p.Cys584Phe)]

NM_001278716.2(FBXL4):c.1751G>T (p.Cys584Phe)

Gene:

FBXL4:F-box and leucine rich repeat protein 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q16.1

Genomic location:

Preferred name:

NM_001278716.2(FBXL4):c.1751G>T (p.Cys584Phe)

HGVS:

NC_000006.12:g.98874393C>A
NG_033903.1:g.78614G>T
NM_001278716.2:c.1751G>TMANE SELECT
NM_012160.5:c.1751G>T
NP_001265645.1:p.Cys584Phe
NP_036292.2:p.Cys584Phe
NP_036292.2:p.Cys584Phe
NC_000006.11:g.99322269C>A
NM_012160.4:c.1751G>T
NR_103836.2:n.1736G>T

Protein change:

C584F

Links:

dbSNP: rs115816653

NCBI 1000 Genomes Browser:

rs115816653

Molecular consequence:

NM_001278716.2:c.1751G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_012160.5:c.1751G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_103836.2:n.1736G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Mitochondrial DNA depletion syndrome 13
Synonyms:: Mitochondrial DNA depletion syndrome 13 (encephalomyopathic type)
Identifiers:: MONDO: MONDO:0014198; MedGen: C3809592; Orphanet: 369897; OMIM: 615471

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000598516	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 10, 2017)	germline	reference population	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000598516

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 10, 2017)

germline

reference population

PubMed (1)
[See all records that cite this PMID]

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	reference population

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine, SCV000598516.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	reference population	PubMed (1)

Description

The NM_012160.4:c.1751G>T (NP_036292.2:p.Cys584Phe) [GRCH38: NC_000006.12:g.98874393C>A] variant in FBXL4 gene is interpretated to be a Uncertain Significance - Insufficient Evidence based on ACMG guidelines (PMID: 25741868). This variant meets one or more of the following evidence codes reported in the ACMG-guideline. PM2:This variant is absent in key population databases. PM5:This variant causes novel missense change at an amino acid residue where a different pathogenic missense change has been seen before. PP3:Computational evidence/predictors indicate the variant has deleterious effect on FBXL4 structure, function, or protein-protein interaction. Based on this evidence code ClinGen Pathogenicity Calculator (PMID:28081714) suggested that the variant is Uncertain Significance - Insufficient Evidence.

#	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: Dec 24, 2023

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