rs1057519732
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_002755.4(MAP2K1):c.370C>A(p.Pro124Thr) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P124S) has been classified as Pathogenic.
Frequency
Consequence
NM_002755.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K1 | NM_002755.4 | c.370C>A | p.Pro124Thr | missense_variant | 3/11 | ENST00000307102.10 | |
MAP2K1 | NM_001411065.1 | c.304C>A | p.Pro102Thr | missense_variant | 3/10 | ||
MAP2K1 | XM_011521783.4 | c.304C>A | p.Pro102Thr | missense_variant | 3/11 | ||
MAP2K1 | XM_017022411.3 | c.370C>A | p.Pro124Thr | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K1 | ENST00000307102.10 | c.370C>A | p.Pro124Thr | missense_variant | 3/11 | 1 | NM_002755.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cardiofaciocutaneous syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 01, 2017 | Likely pathogenicity based on finding it once in our laboratory de novo in a 5-year-old male with global delays, dysmorphism, short stature, failure to thrive, strabismus - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at