chr16-1772956-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_023936.2(MRPS34):c.164G>A(p.Trp55*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000231 in 1,297,392 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_023936.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS34 | NM_023936.2 | c.164G>A | p.Trp55* | stop_gained | Exon 1 of 3 | ENST00000397375.7 | NP_076425.1 | |
EME2 | NM_001257370.2 | c.-272C>T | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000568449.7 | NP_001244299.1 | ||
MRPS34 | NM_001300900.2 | c.164G>A | p.Trp55* | stop_gained | Exon 1 of 3 | NP_001287829.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS34 | ENST00000397375.7 | c.164G>A | p.Trp55* | stop_gained | Exon 1 of 3 | 1 | NM_023936.2 | ENSP00000380531.3 | ||
MRPS34 | ENST00000177742.7 | c.164G>A | p.Trp55* | stop_gained | Exon 1 of 3 | 1 | ENSP00000177742.3 | |||
EME2 | ENST00000568449 | c.-272C>T | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_001257370.2 | ENSP00000457353.1 |
Frequencies
GnomAD3 genomes Cov.: 35
GnomAD4 exome AF: 0.00000231 AC: 3AN: 1297392Hom.: 0 Cov.: 62 AF XY: 0.00000158 AC XY: 1AN XY: 634696
GnomAD4 genome Cov.: 35
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This sequence change creates a premature translational stop signal (p.Trp55*) in the MRPS34 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MRPS34 are known to be pathogenic (PMID: 28777931). 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. For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at