chr16-1772888-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_023936.2(MRPS34):c.232C>T(p.Arg78Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000000771 in 1,297,742 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS34 | NM_023936.2 | c.232C>T | p.Arg78Cys | missense_variant | Exon 1 of 3 | ENST00000397375.7 | NP_076425.1 | |
EME2 | NM_001257370.2 | c.-340G>A | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000568449.7 | NP_001244299.1 | ||
MRPS34 | NM_001300900.2 | c.232C>T | p.Arg78Cys | 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.232C>T | p.Arg78Cys | missense_variant | Exon 1 of 3 | 1 | NM_023936.2 | ENSP00000380531.3 | ||
MRPS34 | ENST00000177742.7 | c.232C>T | p.Arg78Cys | missense_variant | Exon 1 of 3 | 1 | ENSP00000177742.3 | |||
EME2 | ENST00000568449 | c.-340G>A | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_001257370.2 | ENSP00000457353.1 |
Frequencies
GnomAD3 genomes Cov.: 35
GnomAD4 exome AF: 7.71e-7 AC: 1AN: 1297742Hom.: 0 Cov.: 63 AF XY: 0.00 AC XY: 0AN XY: 633858
GnomAD4 genome Cov.: 35
ClinVar
Submissions by phenotype
not provided Uncertain:1
Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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. This variant has not been reported in the literature in individuals affected with MRPS34-related conditions. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 78 of the MRPS34 protein (p.Arg78Cys). This variant is not present in population databases (gnomAD no frequency). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at