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NM_001278716.2(FBXL4):c.1689G>A (p.Gln563=) 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:
RCV000501544.1

Allele description [Variation Report for NM_001278716.2(FBXL4):c.1689G>A (p.Gln563=)]

NM_001278716.2(FBXL4):c.1689G>A (p.Gln563=)

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.1689G>A (p.Gln563=)
HGVS:
  • NC_000006.12:g.98875428C>T
  • NG_033903.1:g.77579G>A
  • NM_001278716.2:c.1689G>AMANE SELECT
  • NM_012160.5:c.1689G>A
  • NP_001265645.1:p.Gln563=
  • NP_036292.2:p.Gln563=
  • NP_036292.2:p.Gln563=
  • NC_000006.11:g.99323304C>T
  • NM_012160.4:c.1689G>A
  • NR_103836.2:n.1674G>A
Links:
dbSNP: rs767302112
NCBI 1000 Genomes Browser:
rs767302112
Molecular consequence:
  • NR_103836.2:n.1674G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001278716.2:c.1689G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_012160.5:c.1689G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000598495Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 10, 2017) 		germlinereference population

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedreference 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, SCV000598495.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedreference population PubMed (1)

Description

The NM_012160.4:c.1689G>A (NP_036292.2:p.Gln563=) [GRCH38: NC_000006.12:g.98875428C>T] variant in FBXL4 gene is interpretated to be a Uncertain Significance - Conflicting 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. BP4:Computational evidence/predictors indicate no impact on the FBXL4 structure, function, or protein-protein interaction. BP7:The variant is silent with non predicted splice impact. Based on this evidence code ClinGen Pathogenicity Calculator (PMID:28081714) suggested that the variant is Uncertain Significance - Conflicting Evidence.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022