10-73250966-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_016065.4(MRPS16):c.300T>A(p.His100Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_016065.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS16 | NM_016065.4 | c.300T>A | p.His100Gln | missense_variant | Exon 3 of 3 | ENST00000372945.8 | NP_057149.1 | |
MRPS16 | XM_047425263.1 | c.294T>A | p.His98Gln | missense_variant | Exon 3 of 3 | XP_047281219.1 | ||
MRPS16 | NM_001410935.1 | c.274+797T>A | intron_variant | Intron 2 of 2 | NP_001397864.1 | |||
DNAJC9-AS1 | NR_038373.1 | n.175+2516A>T | intron_variant | Intron 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:2
This sequence change replaces histidine, which is basic and polar, with glutamine, which is neutral and polar, at codon 100 of the MRPS16 protein (p.His100Gln). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MRPS16-related conditions. ClinVar contains an entry for this variant (Variation ID: 214675). 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. -
p.His100Gln (CAT>CAA): c.300 T>A in exon 3 of the MRPS16 gene (NM_016065.3). A variant of unknown significance in the MRPS16 gene has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The H100Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in MITONUC-MITOP panel(s). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at