chr22-21805852-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP2PP3_Moderate
The NM_002745.5(MAPK1):c.490A>C(p.Lys164Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002745.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
MAPK1 | NM_002745.5 | c.490A>C | p.Lys164Gln | missense_variant, splice_region_variant | 3/9 | ENST00000215832.11 | |
MAPK1 | NM_138957.3 | c.490A>C | p.Lys164Gln | missense_variant, splice_region_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK1 | ENST00000215832.11 | c.490A>C | p.Lys164Gln | missense_variant, splice_region_variant | 3/9 | 1 | NM_002745.5 | P1 | |
MAPK1 | ENST00000398822.7 | c.490A>C | p.Lys164Gln | missense_variant, splice_region_variant | 3/8 | 1 | P1 | ||
MAPK1 | ENST00000544786.1 | c.490A>C | p.Lys164Gln | missense_variant, splice_region_variant | 3/7 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000824 AC: 119AN: 1444906Hom.: 0 Cov.: 30 AF XY: 0.0000668 AC XY: 48AN XY: 718988
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.490A>C (p.K164Q) alteration is located in exon 3 (coding exon 3) of the MAPK1 gene. This alteration results from a A to C substitution at nucleotide position 490, causing the lysine (K) at amino acid position 164 to be replaced by a glutamine (Q). 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
Publications
No publications associated with this variant yet.