12-111880505-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_003668.4(MAPKAPK5):c.638C>T(p.Pro213Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,566 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPKAPK5 | ENST00000550735.7 | c.638C>T | p.Pro213Leu | missense_variant | Exon 8 of 14 | 1 | NM_003668.4 | ENSP00000449667.2 | ||
MAPKAPK5 | ENST00000551404.7 | c.638C>T | p.Pro213Leu | missense_variant | Exon 8 of 14 | 5 | ENSP00000449381.2 | |||
MAPKAPK5 | ENST00000549875.1 | c.191C>T | p.Pro64Leu | missense_variant | Exon 3 of 9 | 5 | ENSP00000473467.1 | |||
MAPKAPK5 | ENST00000553053.5 | n.191C>T | non_coding_transcript_exon_variant | Exon 3 of 7 | 5 | ENSP00000448408.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151960Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249252Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135230
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461606Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 727084
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151960Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.638C>T (p.P213L) alteration is located in exon 8 (coding exon 8) of the MAPKAPK5 gene. This alteration results from a C to T substitution at nucleotide position 638, causing the proline (P) at amino acid position 213 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at