3-131462761-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007208.4(MRPL3):c.1009G>A(p.Val337Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,612,458 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPL3 | NM_007208.4 | c.1009G>A | p.Val337Met | missense_variant | 10/10 | ENST00000264995.8 | NP_009139.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.1009G>A | p.Val337Met | missense_variant | 10/10 | 1 | NM_007208.4 | ENSP00000264995 | P1 | |
MRPL3 | ENST00000425847.6 | c.1090G>A | p.Val364Met | missense_variant | 11/11 | 2 | ENSP00000398536 | |||
MRPL3 | ENST00000511168.5 | c.1054G>A | p.Val352Met | missense_variant | 10/10 | 2 | ENSP00000424107 | |||
MRPL3 | ENST00000510043.1 | n.433G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 250236Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135240
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1460320Hom.: 1 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 726482
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 14, 2022 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with MRPL3-related conditions. This variant is present in population databases (rs141422904, gnomAD 0.05%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 337 of the MRPL3 protein (p.Val337Met). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at