NM_001278716.2(FBXL4):c.415_416insTT (p.Ala139fs) AND Mitochondrial DNA depletion syndrome 13

Germline classification:: Likely pathogenic (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:: RCV000501591.1

Allele description [Variation Report for NM_001278716.2(FBXL4):c.415_416insTT (p.Ala139fs)]

NM_001278716.2(FBXL4):c.415_416insTT (p.Ala139fs)

Gene:

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

Variant type:

Insertion

Cytogenetic location:

6q16.2

Genomic location:

Preferred name:

NM_001278716.2(FBXL4):c.415_416insTT (p.Ala139fs)

HGVS:

NC_000006.12:g.98926573_98926574insAA
NG_033903.1:g.26433_26434insTT
NM_001278716.2:c.415_416insTTMANE SELECT
NM_012160.5:c.415_416insTT
NP_001265645.1:p.Ala139fs
NP_036292.2:p.Ala139fs
NP_036292.2:p.Ala139fs
NC_000006.11:g.99374449_99374450insAA
NM_012160.4:c.415_416insTT
NR_103836.2:n.746_747insTT
NR_103837.2:n.746_747insTT

Protein change:

A139fs

Links:

dbSNP: rs767543583

NCBI 1000 Genomes Browser:

rs767543583

Molecular consequence:

NM_001278716.2:c.415_416insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012160.5:c.415_416insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NR_103836.2:n.746_747insTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_103837.2:n.746_747insTT - 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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109552[uid] AND (alive[prop]) (1)
Gene
Sri sorcin [Mus musculus]
Sri sorcin [Mus musculus]
Gene ID:109552

Gene
LOC109339275 [Lupinus angustifolius]
LOC109339275 [Lupinus angustifolius]
Gene ID:109339275

Gene
LOC109339453 [Lupinus angustifolius]
LOC109339453 [Lupinus angustifolius]
Gene ID:109339453

Gene
B3gntl1 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1 [Mus ...
B3gntl1 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1 [Mus musculus]
Gene ID:210004

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000598272	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (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

SCV000598272

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

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(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, SCV000598272.1

#	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.415_416insTT (NP_036292.2:p.Ala139ValfsTer6) [GRCH38: NC_000006.12:g.98926573_98926574insAA] variant in FBXL4 gene is interpretated to be a Likely Pathogenic based on ACMG guidelines (PMID: 25741868). This variant meets one or more of the following evidence codes reported in the ACMG-guideline. PVS1:This variant is a predcted null variant in FBXL4 where loss of function is a known mechanism of disease. PM2:This variant is absent in key population databases. Based on this evidence code ClinGen Pathogenicity Calculator (PMID:28081714) suggested that the variant is Likely 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: Apr 23, 2022

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