rs28937899
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_025136.4(OPA3):c.415C>T(p.Gln139Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000206 in 1,453,420 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 (★). Synonymous variant affecting the same amino acid position (i.e. Q139Q) has been classified as Likely benign.
Frequency
Consequence
NM_025136.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPA3 | NM_025136.4 | c.415C>T | p.Gln139Ter | stop_gained | 2/2 | ENST00000263275.5 | |
OPA3 | XM_006723403.5 | c.256C>T | p.Gln86Ter | stop_gained | 3/3 | ||
OPA3 | NM_001017989.3 | c.143-24183C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPA3 | ENST00000263275.5 | c.415C>T | p.Gln139Ter | stop_gained | 2/2 | 1 | NM_025136.4 | P1 | |
OPA3 | ENST00000323060.4 | c.143-24183C>T | intron_variant | 1 | |||||
OPA3 | ENST00000544371.1 | c.256C>T | p.Gln86Ter | stop_gained | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1453420Hom.: 0 Cov.: 62 AF XY: 0.00000277 AC XY: 2AN XY: 723058
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
3-Methylglutaconic aciduria type 3 Pathogenic:2Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2008 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Feb 15, 2017 | - - |
not provided, no classification provided | literature only | GeneReviews | - | Found in an individual of Indian origin with Costeff syndrome - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at