22-50524014-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_005138.3(SCO2):c.398G>A(p.Cys133Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,214 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 (no stars). Synonymous variant affecting the same amino acid position (i.e. C133C) has been classified as Likely benign.
Frequency
Consequence
NM_005138.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCO2 | NM_005138.3 | c.398G>A | p.Cys133Tyr | missense_variant | 2/2 | ENST00000395693.8 | |
NCAPH2 | NM_152299.4 | c.*639C>T | 3_prime_UTR_variant | 20/20 | ENST00000420993.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCO2 | ENST00000395693.8 | c.398G>A | p.Cys133Tyr | missense_variant | 2/2 | 1 | NM_005138.3 | P1 | |
NCAPH2 | ENST00000420993.7 | c.*639C>T | 3_prime_UTR_variant | 20/20 | 1 | NM_152299.4 | P4 | ||
ENST00000608319.1 | n.89C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461214Hom.: 0 Cov.: 73 AF XY: 0.00 AC XY: 0AN XY: 726912
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 15, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at