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GeneBe

11-1956383-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_021134.4(MRPL23):c.425C>T(p.Pro142Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 1 hom., cov: 17)
Exomes 𝑓: 0.00012 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MRPL23
NM_021134.4 missense

Scores

2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.15

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.04713735).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.425C>T p.Pro142Leu missense_variant 5/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.425C>T p.Pro142Leu missense_variant 5/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
21
AN:
133338
Hom.:
1
Cov.:
17
FAILED QC
Gnomad AFR
AF:
0.000361
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000825
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000307
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000828
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000121
AC:
29
AN:
239252
Hom.:
0
AF XY:
0.000130
AC XY:
17
AN XY:
130554
show subpopulations
Gnomad AFR exome
AF:
0.000323
Gnomad AMR exome
AF:
0.0000586
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000614
Gnomad SAS exome
AF:
0.0000329
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000551
Gnomad OTH exome
AF:
0.000673
Alfa
AF:
0.000134
Hom.:
0
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.000116
AC:
14
EpiCase
AF:
0.0000546
EpiControl
AF:
0.000119

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 GeneticsNov 29, 2021The c.425C>T (p.P142L) alteration is located in exon 5 (coding exon 5) of the MRPL23 gene. This alteration results from a C to T substitution at nucleotide position 425, causing the proline (P) at amino acid position 142 to be replaced by a leucine (L). 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
-0.44
T
BayesDel_noAF
Benign
-0.50
Cadd
Benign
14
Dann
Benign
0.83
DEOGEN2
Benign
0.022
T;T
Eigen
Benign
-0.61
Eigen_PC
Benign
-0.60
FATHMM_MKL
Benign
0.74
D
M_CAP
Benign
0.021
T
MetaRNN
Benign
0.047
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.0
M;M
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Benign
0.43
T
PROVEAN
Uncertain
-3.9
D;D
REVEL
Benign
0.11
Sift
Benign
0.17
T;T
Sift4G
Benign
0.16
T;T
Polyphen
0.046
B;B
Vest4
0.17
MVP
0.47
MPC
0.17
ClinPred
0.033
T
GERP RS
2.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.072
gMVP
0.37

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

LitVar

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

Other links and lift over

dbSNP: rs140352683; hg19: chr11-1977613; COSMIC: COSV67413629; COSMIC: COSV67413629; API