16-88709982-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP3PP5BP4

The NM_001012759.3(CTU2):​c.188T>C​(p.Leu63Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00105 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L63V) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00056 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 0 hom. )

Consequence

CTU2
NM_001012759.3 missense

Scores

6
7
6

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:2

Conservation

PhyloP100: 5.21
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
Multiple lines of computational evidence support a deleterious effect 6: AlphaMissense, BayesDel_noAF, Cadd, MutationAssessor, PrimateAI, PROVEAN [when BayesDel_addAF, max_spliceai, MetaRNN, MutationTaster was below the threshold]
PP5
Variant 16-88709982-T-C is Pathogenic according to our data. Variant chr16-88709982-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 635410.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Uncertain_significance=1}.
BP4
Computational evidence support a benign effect (MetaRNN=0.23819351). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTU2NM_001012759.3 linkuse as main transcriptc.188T>C p.Leu63Pro missense_variant 3/15 ENST00000453996.7
CTU2NM_001318507.2 linkuse as main transcriptc.188T>C p.Leu63Pro missense_variant 3/15
CTU2NM_001012762.3 linkuse as main transcriptc.188T>C p.Leu63Pro missense_variant 3/14
CTU2NM_001318513.2 linkuse as main transcriptc.-39-241T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTU2ENST00000453996.7 linkuse as main transcriptc.188T>C p.Leu63Pro missense_variant 3/151 NM_001012759.3 P2Q2VPK5-1
ENST00000616106.1 linkuse as main transcriptn.456A>G non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.000565
AC:
86
AN:
152200
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000565
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00106
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000796
AC:
200
AN:
251340
Hom.:
0
AF XY:
0.000795
AC XY:
108
AN XY:
135888
show subpopulations
Gnomad AFR exome
AF:
0.0000616
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00109
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000370
Gnomad NFE exome
AF:
0.00156
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.00110
AC:
1610
AN:
1461634
Hom.:
0
Cov.:
32
AF XY:
0.00104
AC XY:
755
AN XY:
727104
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.000612
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000357
Gnomad4 NFE exome
AF:
0.00136
Gnomad4 OTH exome
AF:
0.000911
GnomAD4 genome
AF:
0.000565
AC:
86
AN:
152318
Hom.:
0
Cov.:
33
AF XY:
0.000483
AC XY:
36
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000565
Gnomad4 NFE
AF:
0.00106
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00129
Hom.:
0
Bravo
AF:
0.000604
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.00104
AC:
4
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00140
AC:
12
ExAC
AF:
0.000980
AC:
119
EpiCase
AF:
0.00153
EpiControl
AF:
0.00119

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingCenter for Genomic Medicine, King Faisal Specialist Hospital and Research Center-- -
CTU2-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesDec 06, 2023The CTU2 c.188T>C variant is predicted to result in the amino acid substitution p.Leu63Pro. This variant in the compound heterozygous condition along with a second variant in this gene was reported in one individual with Intellectual disability (Table 4, Helsmoortel et al. 2015. PubMed ID: 25081361) and was reported in the homozygous condition in two unrelated individuals with DREAM‐PL syndrome (dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly) (Table 1, Shaheen et al. 2019. PubMed ID: 31301155). This variant is reported in 0.15% of alleles in individuals of European (non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 07, 2023This sequence change replaces leucine with proline at codon 63 of the CTU2 protein (p.Leu63Pro). The leucine residue is highly conserved and there is a moderate physicochemical difference between leucine and proline. This variant is present in population databases (rs147948789, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of DREAM-PL (dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly,polydactyly, and lissencephaly) (PMID: 25081361, 31301155). ClinVar contains an entry for this variant (Variation ID: 635410). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CTU2 protein function with a positive predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Benign
-0.035
T
BayesDel_noAF
Pathogenic
0.17
CADD
Pathogenic
30
DANN
Uncertain
1.0
DEOGEN2
Benign
0.24
T;.;.;.
Eigen
Uncertain
0.64
Eigen_PC
Uncertain
0.55
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.83
T;T;D;T
M_CAP
Uncertain
0.27
D
MetaRNN
Benign
0.24
T;T;T;T
MetaSVM
Benign
-0.33
T
MutationAssessor
Pathogenic
3.2
M;M;.;.
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Pathogenic
0.82
D
PROVEAN
Pathogenic
-6.2
D;D;D;D
REVEL
Uncertain
0.61
Sift
Uncertain
0.0020
D;D;D;D
Sift4G
Pathogenic
0.0
D;D;D;D
Polyphen
1.0
D;D;.;.
Vest4
0.95
MVP
0.64
ClinPred
0.42
T
GERP RS
4.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.94
gMVP
0.89

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs147948789; hg19: chr16-88776390; API