19-2046223-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_199054.3(MKNK2):c.302G>A(p.Cys101Tyr) variant causes a missense change. 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 Uncertain significance (★).
Frequency
Consequence
NM_199054.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKNK2 | ENST00000250896.9 | c.302G>A | p.Cys101Tyr | missense_variant | Exon 5 of 14 | 5 | NM_199054.3 | ENSP00000250896.3 | ||
MKNK2 | ENST00000309340.11 | c.302G>A | p.Cys101Tyr | missense_variant | Exon 5 of 14 | 1 | ENSP00000309485.6 | |||
MKNK2 | ENST00000586828.5 | n.241+144G>A | intron_variant | Intron 3 of 11 | 2 | ENSP00000465425.1 | ||||
MKNK2 | ENST00000589509.5 | c.*238G>A | downstream_gene_variant | 5 | ENSP00000466147.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1455750Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 724548
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302G>A (p.C101Y) alteration is located in exon 5 (coding exon 4) of the MKNK2 gene. This alteration results from a G to A substitution at nucleotide position 302, causing the cysteine (C) at amino acid position 101 to be replaced by a tyrosine (Y). 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.