rs886037913
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001243925.2(MAPKAPK3):āc.518T>Cā(p.Leu173Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging 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. L173F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001243925.2 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 |
---|---|---|---|---|---|---|---|
MAPKAPK3 | NM_001243925.2 | c.518T>C | p.Leu173Pro | missense_variant | 6/11 | ENST00000621469.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPKAPK3 | ENST00000621469.5 | c.518T>C | p.Leu173Pro | missense_variant | 6/11 | 1 | NM_001243925.2 | P1 | |
MAPKAPK3 | ENST00000357955.6 | c.518T>C | p.Leu173Pro | missense_variant | 6/11 | 1 | P1 | ||
MAPKAPK3 | ENST00000446044.5 | c.518T>C | p.Leu173Pro | missense_variant | 8/13 | 1 | P1 | ||
MAPKAPK3 | ENST00000430409.5 | c.518T>C | p.Leu173Pro | missense_variant | 6/10 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727230
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Patterned macular dystrophy 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 08, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at