rs368064728
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BS1_Supporting
The NM_030662.4(MAP2K2):c.806C>T(p.Pro269Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000479 in 1,607,542 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P269R) has been classified as Uncertain significance.
Frequency
Consequence
NM_030662.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K2 | NM_030662.4 | c.806C>T | p.Pro269Leu | missense_variant | 7/11 | ENST00000262948.10 | |
MAP2K2 | XM_047439100.1 | c.236C>T | p.Pro79Leu | missense_variant | 5/9 | ||
MAP2K2 | XM_006722799.3 | c.705+1705C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K2 | ENST00000262948.10 | c.806C>T | p.Pro269Leu | missense_variant | 7/11 | 1 | NM_030662.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000170 AC: 4AN: 235910Hom.: 0 AF XY: 0.0000311 AC XY: 4AN XY: 128552
GnomAD4 exome AF: 0.0000515 AC: 75AN: 1455320Hom.: 0 Cov.: 33 AF XY: 0.0000567 AC XY: 41AN XY: 723524
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 30, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 10, 2017 | Variant summary: The MAP2K2 c.806C>T (p.Pro269Leu) variant causes a missense change involving the alteration of a conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). The variant of interest has been found in a large, broad control population, ExAC in 3/80512 control chromosomes at a frequency of 0.0000373, which is approximately 15 times the estimated maximal expected allele frequency of a pathogenic MAP2K2 variant (0.0000025), suggesting this variant is likely a benign polymorphism. This variant was reported in one case of infant ALL without strong evidence for causality (Zhang_BRCA_NEJM_2015). One clinical diagnostic laboratory classified this variant as uncertain significance (cited as a maternally inherited variant identified in pt in NSRD panel; no clinical info on pt and the mother provided by submitter). Taken together, this variant is classified as VUS-possibly benign. - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 04, 2015 | p.Pro269Leu (CCG>CTG): c.806 C>T in exon 7 of the MAP2K2 gene (NM_030662.3).A variant of unknown significance has been identified in the MAP2K2 gene. The P269L variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The P269L variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The P269L variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is well conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. One missense mutation in a nearby residue (K273R) has been reported in association with Cardio-Facio-Cutaneous (CFC) syndrome, supporting the functional importance of this region of the protein. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant.This variant has been observed to be maternally inherited. The variant is found in NOONAN panel(s). - |
RASopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is not expected to disrupt MAP2K2 function. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 269 of the MAP2K2 protein (p.Pro269Leu). This variant is present in population databases (rs368064728, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with MAP2K2-related conditions. ClinVar contains an entry for this variant (Variation ID: 180906). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at