6-151405236-C-G
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PM4PP5_Very_Strong
The NM_017909.4(RMND1):āc.1349G>Cā(p.Ter450Serext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,612,142 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 Likely pathogenic (ā ā ).
Frequency
Consequence
NM_017909.4 stop_lost
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 |
---|---|---|---|---|---|---|---|---|
RMND1 | NM_017909.4 | c.1349G>C | p.Ter450Serext*? | stop_lost | Exon 12 of 12 | ENST00000444024.3 | NP_060379.2 | |
RMND1 | NM_001271937.2 | c.839G>C | p.Ter280Serext*? | stop_lost | Exon 11 of 11 | NP_001258866.1 | ||
RMND1 | XM_047418959.1 | c.1349G>C | p.Ter450Serext*? | stop_lost | Exon 12 of 13 | XP_047274915.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250924Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135676
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459918Hom.: 0 Cov.: 29 AF XY: 0.0000193 AC XY: 14AN XY: 726434
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74446
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 11 Pathogenic:4Uncertain:1
A Homozygote Stop readthrough variant c.1349G>C in Exon 12 of the RMND1 gene that results in the amino acid substitution p.Ter450Serext*? was identified. The observed variant has a minor allele frequency of 0.00002% in gnomAD exomes and novel is gnomAD genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic [Variation ID: 143051]. The observed variation has been reported in mitochondrial disorders patients (Vinu N, et.al, 2018). For these reasons, this variant has been classified as Pathogenic. -
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This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
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Inborn genetic diseases Pathogenic:1
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Mitochondrial disease Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at