16-1772890-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_023936.2(MRPS34):c.230G>A(p.Gly77Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000207 in 1,452,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023936.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS34 | NM_023936.2 | c.230G>A | p.Gly77Asp | missense_variant | Exon 1 of 3 | ENST00000397375.7 | NP_076425.1 | |
EME2 | NM_001257370.2 | c.-338C>T | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000568449.7 | NP_001244299.1 | ||
MRPS34 | NM_001300900.2 | c.230G>A | p.Gly77Asp | missense_variant | Exon 1 of 3 | NP_001287829.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS34 | ENST00000397375.7 | c.230G>A | p.Gly77Asp | missense_variant | Exon 1 of 3 | 1 | NM_023936.2 | ENSP00000380531.3 | ||
MRPS34 | ENST00000177742.7 | c.230G>A | p.Gly77Asp | missense_variant | Exon 1 of 3 | 1 | ENSP00000177742.3 | |||
EME2 | ENST00000568449 | c.-338C>T | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_001257370.2 | ENSP00000457353.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 35
GnomAD4 exome AF: 0.00000154 AC: 2AN: 1300406Hom.: 0 Cov.: 63 AF XY: 0.00000315 AC XY: 2AN XY: 635500
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 74390
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 77 of the MRPS34 protein (p.Gly77Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MRPS34-related conditions. ClinVar contains an entry for this variant (Variation ID: 2422099). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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