Table 1.

List of the Identified Pathogenic MAPK1 Missense Variants

Nucleotide Change	Amino Acid Change	Domain	Mutation Class	Subject	Origin	REVELa	CADD phreda	Metadome dN/dSb	ACMGc
c.221T>A	p.Ile74Asn	active site	2	7	de novo	0.82	29.0	0.21	pathogenic
c.238C>T	p.His80Tyr	DRS	1	3	de novo	0.88	30.0	0.27	pathogenic
c.521C>T	p.Ala174Val	activation lip	2	1	de novo	0.45	23.9	0.10	pathogenic
c.952G>A	p.Asp318Asn	DRS	1	4	de novo	0.31	28.9	0.27	pathogenic
c.953A>G	p.Asp318Gly	DRS	1	2	de novo	0.39	25.7		pathogenic
c.964G>C	p.Glu322Gln	DRS	1	6	de novo	0.31	26.7	0.19	pathogenic
c.968C>G	p.Pro323Arg	DRS	1	5	de novo	0.73	28.2	0.18	pathogenic

Nucleotide numbering reflects cDNA numbering with 1 corresponding to the A of the ATG translation initiation codon in the MAPK1 reference sequence (GenBank: NM_002745.4). No variants were reported in the public databases ExAC and gnomAD.

^aAll variants were predicted to be “deleterious” by Rare Exome Variant Ensemble Learner (REVEL) and/or Combined Annotation Dependent Depletion (CADD) v.1.3 algorithms.^43,44 Scores > 15 (CADDphred) or > 0.5 (REVEL) predict that the sequence change has a significant impact on protein structure and function.

^bd_N/d_S metric detects evolutionary pressure in protein-coding regions and genomes and is used to measure genetic tolerance.⁴⁵ Residues with d_N/d_S values < 0.53 are considered to map within regions “intolerant” to nonsynonymous variation, those with a ratio < 0.18 are supposed to be within “highly intolerant” regions (see Figure S2).

^cAll changes satisfied the necessary criteria to be classified as pathogenic according to the American College of Medical Genetics criteria (see InterVar in Web Resources).⁴⁶ c.221T>A: PS2, PS3, PM1, PM2, PP2, PP3. c.238C>T: PS2, PS3, PM1, PM2, PP2, PP3. c.521C>T: PS2, PS3, PM1, PM2, PP2, PP3. c.952G>A: PS2, PS3, PM1, PM2, PP2, PP3. c.953A>G: PS2, PS3, PM1, PM2, PP2, PP3. c.964G>C: PS2, PS3, PM1, PM2, PM5, PP2, PP3. c.968C>G: PS2, PS3, PM1, PM2, PP2, PP3.