20-31640005-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032609.3(COX4I2):c.155C>A(p.Pro52His) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,272 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P52S) has been classified as Uncertain significance.
Frequency
Consequence
NM_032609.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COX4I2 | NM_032609.3 | c.155C>A | p.Pro52His | missense_variant | Exon 3 of 5 | ENST00000376075.4 | NP_115998.2 | |
COX4I2 | XM_005260579.5 | c.170C>A | p.Pro57His | missense_variant | Exon 2 of 4 | XP_005260636.1 | ||
COX4I2 | XM_005260580.5 | c.170C>A | p.Pro57His | missense_variant | Exon 2 of 3 | XP_005260637.1 | ||
COX4I2 | XM_005260581.4 | c.155C>A | p.Pro52His | missense_variant | Exon 3 of 4 | XP_005260638.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251160Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135742
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with histidine, which is basic and polar, at codon 52 of the COX4I2 protein (p.Pro52His). This variant is present in population databases (rs575560908, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with COX4I2-related conditions. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at