NM_018006.5(TRMU):c.4C>T (p.Gln2Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 25, 2021
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:: RCV001890520.4

Allele description [Variation Report for NM_018006.5(TRMU):c.4C>T (p.Gln2Ter)]

NM_018006.5(TRMU):c.4C>T (p.Gln2Ter)

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.4C>T (p.Gln2Ter)

HGVS:

NC_000022.11:g.46335768C>T
NG_012173.1:g.5368C>T
NM_001282782.2:c.-232C>T
NM_001282783.2:c.-251C>T
NM_001282784.2:c.-251C>T
NM_001282785.2:c.4C>T
NM_018006.5:c.4C>TMANE SELECT
NP_001269714.1:p.Gln2Ter
NP_060476.2:p.Gln2Ter
NC_000022.10:g.46731665C>T
NR_104240.2:n.55C>T
NR_104241.2:n.55C>T

Protein change:

Q2*

Links:

dbSNP: rs1464059546

NCBI 1000 Genomes Browser:

rs1464059546

Molecular consequence:

NM_001282782.2:c.-232C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282783.2:c.-251C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282784.2:c.-251C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_104240.2:n.55C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104241.2:n.55C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001282785.2:c.4C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_018006.5:c.4C>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
SCV002155324	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 25, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19732863, 23625533, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002155324

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 25, 2021)

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

Acute infantile liver failure due to mutations in the TRMU gene.

Zeharia A, Shaag A, Pappo O, Mager-Heckel AM, Saada A, Beinat M, Karicheva O, Mandel H, Ofek N, Segel R, Marom D, Rötig A, Tarassov I, Elpeleg O.

Am J Hum Genet. 2009 Sep;85(3):401-7. doi: 10.1016/j.ajhg.2009.08.004. Erratum in: Am J Hum Genet. 2010 Feb;86(2):295.

PubMed [citation]

PMID:: 19732863
PMCID:: PMC2771591

Mitochondrial Infantile Liver Disease due to TRMU Gene Mutations: Three New Cases.

Gaignard P, Gonzales E, Ackermann O, Labrune P, Correia I, Therond P, Jacquemin E, Slama A.

JIMD Rep. 2013;11:117-23. doi: 10.1007/8904_2013_230. Epub 2013 Apr 27.

PubMed [citation]

PMID:: 23625533
PMCID:: PMC3755544

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002155324.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with TRMU-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change creates a premature translational stop signal (p.Gln2*) in the TRMU gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TRMU are known to be pathogenic (PMID: 19732863, 23625533).

#	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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