rs771914518
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007208.4(MRPL3):c.824G>A(p.Arg275Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000209 in 1,582,114 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_007208.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.824G>A | p.Arg275Lys | missense_variant | Exon 9 of 10 | 1 | NM_007208.4 | ENSP00000264995.2 | ||
MRPL3 | ENST00000425847.6 | c.905G>A | p.Arg302Lys | missense_variant | Exon 10 of 11 | 2 | ENSP00000398536.2 | |||
MRPL3 | ENST00000511168.5 | c.866G>A | p.Arg289Lys | missense_variant | Exon 9 of 10 | 2 | ENSP00000424107.1 | |||
MRPL3 | ENST00000510043.1 | n.248G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000790 AC: 12AN: 151822Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000312 AC: 7AN: 224464Hom.: 0 AF XY: 0.0000246 AC XY: 3AN XY: 121926
GnomAD4 exome AF: 0.0000147 AC: 21AN: 1430292Hom.: 0 Cov.: 29 AF XY: 0.00000844 AC XY: 6AN XY: 711304
GnomAD4 genome AF: 0.0000790 AC: 12AN: 151822Hom.: 0 Cov.: 32 AF XY: 0.0000944 AC XY: 7AN XY: 74128
ClinVar
Submissions by phenotype
not provided Uncertain:2
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 275 of the MRPL3 protein (p.Arg275Lys). This variant is present in population databases (rs771914518, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with MRPL3-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MRPL3 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at