8-120432042-G-A

Variant summary

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

The NM_014078.6(MRPL13):​c.233C>T​(p.Ser78Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,404 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 Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

MRPL13
NM_014078.6 missense

Scores

3
5
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.46
Variant links:
Genes affected
MRPL13 (HGNC:14278): (mitochondrial ribosomal protein L13) 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 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=0.3411808).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MRPL13NM_014078.6 linkc.233C>T p.Ser78Phe missense_variant Exon 3 of 7 ENST00000306185.8 NP_054797.2 Q9BYD1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MRPL13ENST00000306185.8 linkc.233C>T p.Ser78Phe missense_variant Exon 3 of 7 1 NM_014078.6 ENSP00000306548.3 Q9BYD1
MRPL13ENST00000518696.5 linkn.152-6676C>T intron_variant Intron 2 of 5 1 ENSP00000428867.1 E5RFI2
MRPL13ENST00000518918.1 linkc.161C>T p.Ser54Phe missense_variant Exon 3 of 6 2 ENSP00000430545.1 E5RJI7
MRPL13ENST00000520677.1 linkn.157-6676C>T intron_variant Intron 2 of 3 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000409
AC:
1
AN:
244250
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
132052
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000561
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.90e-7
AC:
1
AN:
1449404
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
721000
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Jun 17, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.233C>T (p.S78F) alteration is located in exon 3 (coding exon 3) of the MRPL13 gene. This alteration results from a C to T substitution at nucleotide position 233, causing the serine (S) at amino acid position 78 to be replaced by a phenylalanine (F). 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
Uncertain
0.42
BayesDel_addAF
Pathogenic
0.23
D
BayesDel_noAF
Pathogenic
0.26
CADD
Benign
23
DANN
Benign
0.82
DEOGEN2
Benign
0.10
T;.
Eigen
Benign
0.030
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.90
D;D
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.34
T;T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
0.63
N;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
1.9
N;N
REVEL
Uncertain
0.42
Sift
Benign
0.97
T;T
Sift4G
Benign
0.70
T;.
Polyphen
0.037
B;.
Vest4
0.85
MutPred
0.53
Loss of disorder (P = 0.0012);.;
MVP
0.47
MPC
0.23
ClinPred
0.42
T
GERP RS
6.0
Varity_R
0.40
gMVP
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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: rs1189076442; hg19: chr8-121444282; COSMIC: COSV60367245; API