11-65125520-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_004927.4(MRPL49):c.262C>T(p.Arg88Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000304 in 1,613,940 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 Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R88H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_004927.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPL49 | NM_004927.4 | c.262C>T | p.Arg88Cys | missense_variant | Exon 3 of 4 | ENST00000279242.7 | NP_004918.1 | |
MRPL49 | NR_037567.1 | n.342C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | ||||
MRPL49 | NR_037568.2 | n.137C>T | non_coding_transcript_exon_variant | Exon 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251392Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135874
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461834Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727222
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
Perrault syndrome 1 Pathogenic:1
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COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 60 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at