NM_207346.3(TSEN54):c.940del (p.Leu314fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 20, 2023
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:: RCV003768038.1

Allele description [Variation Report for NM_207346.3(TSEN54):c.940del (p.Leu314fs)]

NM_207346.3(TSEN54):c.940del (p.Leu314fs)

Gene:

TSEN54:tRNA splicing endonuclease subunit 54 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_207346.3(TSEN54):c.940del (p.Leu314fs)

HGVS:

NC_000017.11:g.75522021del
NG_013041.1:g.10494del
NM_207346.3:c.940delMANE SELECT
NP_997229.2:p.Leu314fs
NC_000017.10:g.73518100del
NC_000017.10:g.73518102del
NM_207346.2:c.938delC

Protein change:

L314fs

Links:

dbSNP: rs1012275384

NCBI 1000 Genomes Browser:

rs1012275384

Molecular consequence:

NM_207346.3:c.940del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

WARS2P1 tryptophanyl tRNA synthetase 2 pseudogene 1 [Homo sapiens]
WARS2P1 tryptophanyl tRNA synthetase 2 pseudogene 1 [Homo sapiens]
Gene ID:100421633

Gene
WARS2P1 AND (alive[prop]) (1)
Gene
N4bp3 NEDD4 binding protein 3 [Mus musculus]
N4bp3 NEDD4 binding protein 3 [Mus musculus]
Gene ID:212706

Gene
212706[uid] AND (alive[prop]) (1)
Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004694823	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 20, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18711368, 20952379, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004694823

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 20, 2023)

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

tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia.

Budde BS, Namavar Y, Barth PG, Poll-The BT, Nürnberg G, Becker C, van Ruissen F, Weterman MA, Fluiter K, te Beek ET, Aronica E, van der Knaap MS, Höhne W, Toliat MR, Crow YJ, Steinling M, Voit T, Roelenso F, Brussel W, Brockmann K, Kyllerman M, Boltshauser E, et al.

Nat Genet. 2008 Sep;40(9):1113-8. doi: 10.1038/ng.204.

PubMed [citation]

PMID:: 18711368

Clinical, neuroradiological and genetic findings in pontocerebellar hypoplasia.

Namavar Y, Barth PG, Kasher PR, van Ruissen F, Brockmann K, Bernert G, Writzl K, Ventura K, Cheng EY, Ferriero DM, Basel-Vanagaite L, Eggens VR, Krägeloh-Mann I, De Meirleir L, King M, Graham JM Jr, von Moers A, Knoers N, Sztriha L, Korinthenberg R; PCH Consortium., Dobyns WB, et al.

Brain. 2011 Jan;134(Pt 1):143-56. doi: 10.1093/brain/awq287. Epub 2010 Oct 15.

PubMed [citation]

PMID:: 20952379
PMCID:: PMC9136852

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004694823.1

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

Description

This sequence change creates a premature translational stop signal (p.Leu314Phefs*28) in the TSEN54 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TSEN54 are known to be pathogenic (PMID: 18711368, 20952379). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with TSEN54-related conditions. ClinVar contains an entry for this variant (Variation ID: 561138). For these reasons, this variant has been classified as 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: Mar 5, 2024

ClinVar

Relating variation to medicine