NM_207346.3(TSEN54):c.580dup (p.Glu194fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 22, 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:: RCV002706248.3

Allele description [Variation Report for NM_207346.3(TSEN54):c.580dup (p.Glu194fs)]

NM_207346.3(TSEN54):c.580dup (p.Glu194fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_207346.3(TSEN54):c.580dup (p.Glu194fs)

HGVS:

NC_000017.11:g.75521467dup
NG_013041.1:g.9940dup
NM_207346.3:c.580dupMANE SELECT
NP_997229.2:p.Glu194fs
NC_000017.10:g.73517546_73517547insG
NC_000017.10:g.73517548dup

Protein change:

E194fs

Molecular consequence:

NM_207346.3:c.580dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MAG: hypothetical protein A3D84_04745 [Candidatus Woesebacteria bacterium RIFCSP...
MAG: hypothetical protein A3D84_04745 [Candidatus Woesebacteria bacterium RIFCSPHIGHO2_02_FULL_42_20]
gi|1084247774|gb|OGM35033.1||gnl|WG S|A3D84_04745

Protein
MAG: hypothetical protein A3D84_05585 [Candidatus Woesebacteria bacterium RIFCSP...
MAG: hypothetical protein A3D84_05585 [Candidatus Woesebacteria bacterium RIFCSPHIGHO2_02_FULL_42_20]
gi|1084248271|gb|OGM35515.1||gnl|WG S|A3D84_05585

Protein
Homo sapiens NOL1/NOP2/Sun domain family, member 2, mRNA (cDNA clone IMAGE:35050...
Homo sapiens NOL1/NOP2/Sun domain family, member 2, mRNA (cDNA clone IMAGE:3505076), partial cds
gi|33875910|gb|BC001041.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002996134	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 22, 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

SCV002996134

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 22, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002996134.2

#	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.Glu194Glyfs*18) 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 (rs747549006, gnomAD 0.006%). 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: 1957365). 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: Sep 29, 2024

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