NM_018006.5(TRMU):c.10T>G (p.Leu4Val) AND Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Apr 27, 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:: RCV000389480.6

Allele description [Variation Report for NM_018006.5(TRMU):c.10T>G (p.Leu4Val)]

NM_018006.5(TRMU):c.10T>G (p.Leu4Val)

Gene:

TRMU:tRNA mitochondrial 2-thiouridylase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.31

Genomic location:

Preferred name:

NM_018006.5(TRMU):c.10T>G (p.Leu4Val)

Other names:

p.L4V:TTG>GTG

HGVS:

NC_000022.11:g.46335774T>G
NG_012173.1:g.5374T>G
NM_001282782.2:c.-226T>G
NM_001282783.2:c.-245T>G
NM_001282784.2:c.-245T>G
NM_001282785.2:c.10T>G
NM_018006.5:c.10T>GMANE SELECT
NP_001269714.1:p.Leu4Val
NP_060476.2:p.Leu4Val
NC_000022.10:g.46731671T>G
NM_018006.4:c.10T>G
NR_104240.2:n.61T>G
NR_104241.2:n.61T>G

Protein change:

L4V

Links:

dbSNP: rs114302881

NCBI 1000 Genomes Browser:

rs114302881

Molecular consequence:

NM_001282782.2:c.-226T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282783.2:c.-245T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282784.2:c.-245T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282785.2:c.10T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_018006.5:c.10T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_104240.2:n.61T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104241.2:n.61T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins
Synonyms:: Liver failure acute infantile; LIVER FAILURE, INFANTILE, TRANSIENT
Identifiers:: MONDO: MONDO:0013111; MedGen: C3278664; Orphanet: 217371; OMIM: 613070

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000439112	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV001457196	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000439112

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV001457196

Natera, Inc.

no assertion criteria provided

Benign
(Sep 16, 2020)

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000439112.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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., SCV001457196.1

#	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: Dec 24, 2023

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