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GeneBe

11-1952201-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3

The NM_021134.4(MRPL23):c.215T>A(p.Val72Glu) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 1)

Consequence

MRPL23
NM_021134.4 missense

Scores

5
9
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.59

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.836

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.215T>A p.Val72Glu missense_variant 3/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.215T>A p.Val72Glu missense_variant 3/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
Cov.:
1

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 03, 2022The c.215T>A (p.V72E) alteration is located in exon 3 (coding exon 3) of the MRPL23 gene. This alteration results from a T to A substitution at nucleotide position 215, causing the valine (V) at amino acid position 72 to be replaced by a glutamic acid (E). 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
Pathogenic
0.90
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.080
Cadd
Uncertain
25
Dann
Uncertain
0.99
DEOGEN2
Benign
0.22
T;T;T;T;T
Eigen
Uncertain
0.38
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Uncertain
0.94
D
M_CAP
Benign
0.082
D
MetaRNN
Pathogenic
0.84
D;D;D;D;D
MetaSVM
Benign
-0.66
T
MutationAssessor
Uncertain
2.1
M;M;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Uncertain
0.68
T
PROVEAN
Pathogenic
-5.7
D;D;D;D;D
REVEL
Uncertain
0.34
Sift
Pathogenic
0.0
D;D;D;D;D
Sift4G
Pathogenic
0.0010
D;D;D;D;D
Polyphen
1.0
D;D;.;.;.
Vest4
0.80
MutPred
0.57
Gain of disorder (P = 0.0102);Gain of disorder (P = 0.0102);Gain of disorder (P = 0.0102);Gain of disorder (P = 0.0102);Gain of disorder (P = 0.0102);
MVP
0.56
MPC
0.87
ClinPred
0.99
D
GERP RS
3.9
Varity_R
0.96
gMVP
0.54

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: chr11-1973431; API