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GeneBe

X-129907402-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_006649.4(UTP14A):c.62A>T(p.Asp21Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 22)

Consequence

UTP14A
NM_006649.4 missense

Scores

2
5
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.15
Variant links:
Genes affected
UTP14A (HGNC:10665): (UTP14A small subunit processome component) This gene encodes a member of the uridine triphosphate 14 family. As an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA, the encoded protein is involved in ribosome biogenesis and 18S rRNA synthesis. An autosomal retrotransposed copy of this X-linked gene exists on chromosome 13. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.41889098).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UTP14ANM_006649.4 linkuse as main transcriptc.62A>T p.Asp21Val missense_variant 2/15 ENST00000394422.8
LOC105373335XR_007068332.1 linkuse as main transcriptn.2250+1065T>A intron_variant, non_coding_transcript_variant
UTP14ANM_001166221.2 linkuse as main transcriptc.62A>T p.Asp21Val missense_variant 2/14
LOC105373335XR_007068330.1 linkuse as main transcriptn.2329+986T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UTP14AENST00000394422.8 linkuse as main transcriptc.62A>T p.Asp21Val missense_variant 2/151 NM_006649.4 P1Q9BVJ6-1
ENST00000432062.1 linkuse as main transcriptn.293+1065T>A intron_variant, non_coding_transcript_variant 2
UTP14AENST00000425117.6 linkuse as main transcriptc.62A>T p.Asp21Val missense_variant 2/142 Q9BVJ6-3
ENST00000660217.1 linkuse as main transcriptn.1303T>A non_coding_transcript_exon_variant 3/3

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 22, 2024The c.62A>T (p.D21V) alteration is located in exon 2 (coding exon 2) of the UTP14A gene. This alteration results from a A to T substitution at nucleotide position 62, causing the aspartic acid (D) at amino acid position 21 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.031
T
BayesDel_noAF
Benign
-0.28
Cadd
Uncertain
24
Dann
Uncertain
0.99
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.94
D;D
M_CAP
Pathogenic
0.45
D
MetaRNN
Benign
0.42
T;T
MetaSVM
Benign
-0.81
T
MutationAssessor
Pathogenic
3.2
M;M
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-2.3
N;D
REVEL
Benign
0.18
Sift
Uncertain
0.0010
D;D
Sift4G
Uncertain
0.015
D;D
Polyphen
1.0
.;D
Vest4
0.45
MutPred
0.26
Gain of methylation at K24 (P = 0.0375);Gain of methylation at K24 (P = 0.0375);
MVP
0.58
MPC
1.2
ClinPred
0.97
D
GERP RS
5.4
Varity_R
0.28
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-129041378; API