22-50523738-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_005138.3(SCO2):c.674C>T(p.Ser225Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S225C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005138.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCO2 | NM_005138.3 | c.674C>T | p.Ser225Phe | missense_variant | 2/2 | ENST00000395693.8 | |
NCAPH2 | NM_152299.4 | c.*363G>A | 3_prime_UTR_variant | 20/20 | ENST00000420993.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCO2 | ENST00000395693.8 | c.674C>T | p.Ser225Phe | missense_variant | 2/2 | 1 | NM_005138.3 | P1 | |
NCAPH2 | ENST00000420993.7 | c.*363G>A | 3_prime_UTR_variant | 20/20 | 1 | NM_152299.4 | P4 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at