GeneBe

rs942435161

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014763.4(MRPL19):​c.76C>G​(p.Leu26Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

MRPL19
NM_014763.4 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.177

Publications

0 publications found
Variant links:
Genes affected
MRPL19 (HGNC:14052): (mitochondrial ribosomal protein L19) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06785205).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014763.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MRPL19
NM_014763.4
MANE Select
c.76C>Gp.Leu26Val
missense
Exon 1 of 6NP_055578.2P49406

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MRPL19
ENST00000393909.7
TSL:1 MANE Select
c.76C>Gp.Leu26Val
missense
Exon 1 of 6ENSP00000377486.2P49406
MRPL19
ENST00000409374.5
TSL:5
c.76C>Gp.Leu26Val
missense
Exon 1 of 7ENSP00000387284.1P49406
MRPL19
ENST00000884931.1
c.76C>Gp.Leu26Val
missense
Exon 1 of 7ENSP00000554990.1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.0000302

ClinVar

ClinVar submissions as Germline
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
11
DANN
Benign
0.81
DEOGEN2
Benign
0.011
T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.019
N
LIST_S2
Benign
0.68
T
M_CAP
Benign
0.0048
T
MetaRNN
Benign
0.068
T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
1.9
L
PhyloP100
-0.18
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-0.55
N
REVEL
Benign
0.029
Sift
Benign
0.058
T
Sift4G
Benign
0.22
T
Polyphen
0.012
B
Vest4
0.24
MutPred
0.22
Gain of MoRF binding (P = 0.0785)
MVP
0.25
MPC
0.10
ClinPred
0.086
T
GERP RS
0.88
PromoterAI
-0.033
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.054
gMVP
0.35
Mutation Taster
=97/3
polymorphism

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

Other links and lift over

dbSNP: rs942435161; hg19: chr2-75874009; API