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NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 19, 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:
RCV000623727.8

Allele description [Variation Report for NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser)]

NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser)

Gene:
TSEN54:tRNA splicing endonuclease subunit 54 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.1
Genomic location:
Preferred name:
NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser)
HGVS:
  • NC_000017.11:g.75522000G>T
  • NG_013041.1:g.10473G>T
  • NM_207346.3:c.919G>TMANE SELECT
  • NP_997229.2:p.Ala307Ser
  • NC_000017.10:g.73518081G>T
  • NM_207346.2:c.919G>T
  • Q7Z6J9:p.Ala307Ser
Protein change:
A307S; ALA307SER
Links:
UniProtKB: Q7Z6J9#VAR_054813; OMIM: 608755.0001; OMIM: 608755.0002; dbSNP: rs113994152
NCBI 1000 Genomes Browser:
rs113994152
Molecular consequence:
  • NM_207346.3:c.919G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000741184Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Mar 19, 2021) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Severe, fetal-onset form of olivopontocerebellar hypoplasia in three sibs: PCH type 5?

Patel MS, Becker LE, Toi A, Armstrong DL, Chitayat D.

Am J Med Genet A. 2006 Mar 15;140(6):594-603.

PubMed [citation]
PMID:
16470708

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
See all PubMed Citations (5)

Details of each submission

From Ambry Genetics, SCV000741184.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

The c.919G>T (p.A307S) alteration is located in coding exon 8 of the TSEN54 gene. This alteration results from a G to T substitution at nucleotide position 919, causing the alanine (A) at amino acid position 307 to be replaced by a serine (S). Based on data from gnomAD, the T allele has an overall frequency of 0.088% (213/240704) total alleles studied. The highest observed frequency was 0.173% (183/105724) of European (non-Finnish) alleles. This mutation is the most common variant causing TSEN54-related pontocerebellar hypoplasia, found in more than 90% of patients (Budde, 2008; Cassandrini, 2010; Namavar, 2011). This amino acid position is not well conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024