Variant rs149847195 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1

The NM_001012759.3(CTU2):c.1097+2_1097+5delTGTG variant causes a splice donor, splice region, intron change. 1/1 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

CTU2
NM_001012759.3 splice_donor, splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.54

Variant links:

Genes affected

CTU2 (HGNC:28005): (cytosolic thiouridylase subunit 2) This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

CTU2 links:

CTU2 (HGNC:):

CTU2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 3.1, offset of 2, new splice context is: gggGTgtgt. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CTU2	NM_001012759.3 linkuse as main transcript	c.1097+2_1097+5delTGTG	splice_donor_variant, splice_region_variant, intron_variant	ENST00000453996.7	NP_001012777.1	Q2VPK5-1
CTU2	NM_001318507.2 linkuse as main transcript	c.1310+2_1310+5delTGTG	splice_donor_variant, splice_region_variant, intron_variant		NP_001305436.1	Q2VPK5H3BSW6
CTU2	NM_001012762.3 linkuse as main transcript	c.1097+2_1097+5delTGTG	splice_donor_variant, splice_region_variant, intron_variant		NP_001012780.1	Q2VPK5-5
CTU2	NM_001318513.2 linkuse as main transcript	c.836+2_836+5delTGTG	splice_donor_variant, splice_region_variant, intron_variant		NP_001305442.1	Q2VPK5-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTU2	ENST00000453996.7 linkuse as main transcript	c.1097+2_1097+5delTGTG		splice_donor_variant, splice_region_variant, intron_variant		1	NM_001012759.3	ENSP00000388320.2		Q2VPK5-1

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.95

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.63

Position offset: 6

DS_DL_spliceai