rs121434499
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PS4_ModeratePM2PP2PP3PM1
This summary comes from the ClinGen Evidence Repository: The c.400T>C (p.Tyr134His) variant in MAP2K2 was absent from large population studies (PM2). It has been identified in 3 patients with Cardiofaciocutaneous syndrome and 1 with Noonan syndrome (PS4_Moderate; SCV000063166.5, Hopital Universitaire Robert Debre internal data, PMIDs: 18042262, 27763634)Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K2 (PM1; PMID 29493581). Moreover, a different pathogenic missense variant (p.Tyr134Cys) has been previously identified at this codon of MAP2K2 which may indicate that this residue is critical to the function of the protein (PM5 not met; ClinVar 177868). The variant is located in the MAP2K2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Tyr134His variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM2, PS4_Moderate, PM1, PP2, PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA119417/MONDO:0021060/004
Frequency
Consequence
NM_030662.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP2K2 | NM_030662.4 | c.400T>C | p.Tyr134His | missense_variant | 3/11 | ENST00000262948.10 | NP_109587.1 | |
MAP2K2 | XM_006722799.3 | c.400T>C | p.Tyr134His | missense_variant | 3/9 | XP_006722862.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP2K2 | ENST00000262948.10 | c.400T>C | p.Tyr134His | missense_variant | 3/11 | 1 | NM_030662.4 | ENSP00000262948.4 | ||
MAP2K2 | ENST00000394867.9 | n.839T>C | non_coding_transcript_exon_variant | 2/10 | 5 | |||||
MAP2K2 | ENST00000599345.1 | n.597T>C | non_coding_transcript_exon_variant | 3/7 | 5 | |||||
MAP2K2 | ENST00000687128.1 | n.839T>C | non_coding_transcript_exon_variant | 2/7 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Feb 23, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 03, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 18042262, 24803665, 27763634, 33153128, 33258288, 30867592, 18456719, 19156172, 22177953, 22753777, 26399658, 29493581) - |
Cardiofaciocutaneous syndrome 4 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2008 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 18, 2017 | - - |
RASopathy Pathogenic:2
Likely pathogenic, reviewed by expert panel | curation | ClinGen RASopathy Variant Curation Expert Panel | May 09, 2017 | The c.400T>C (p.Tyr134His) variant in MAP2K2 has been identified in patients with clinical features of a RASopathy (PS4_Supporting; PMID 18042262; GeneDx, Partners LMM, University of Magdeburg internal data; GTR Lab ID: 26957, 21766, 506381 ClinVar SCV000063166.5). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). A different pathogenic missense variant (p.Tyr134Cys) has been previously identified at this codon of MAP2K2 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 177868). The variant is located in the MAP2K2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K2 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Tyr134His variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM2, PM5, PP2, PM1, PP3. - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 14, 2023 | This variant disrupts the p.Tyr134 amino acid residue in MAP2K2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 18039235, 18413255, 23885229). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is expected to disrupt MAP2K2 function. ClinVar contains an entry for this variant (Variation ID: 8274). This missense change has been observed in individual(s) with cardio-facio-cutaneous syndrome (PMID: 18042262, 18456719). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 134 of the MAP2K2 protein (p.Tyr134His). For these reasons, this variant has been classified as Pathogenic. - |
MAP2K2-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 01, 2023 | The MAP2K2 c.400T>C variant is predicted to result in the amino acid substitution p.Tyr134His. This variant has been reported in individuals with cardio-facio-cutaneous (CFC) syndrome, Noonan syndrome, or a RASopathy (Nyström et al. 2008. PubMed ID: 18456719; Schulz et al. 2008. PubMed ID: 18042262; Terao et al. 2010. PubMed ID: 20518782; Table S1, Bhoj et al. 2017. PubMed ID: 27763634). This variant was reported in at least one of those patients in the de novo state (Nyström et al. 2008. PubMed ID: 18456719). This variant was also reported de novo in an individual with neurodevelopmental disorder, seizure, other neurological anomaly, syndromic/malformative, immune/hematological diseases, cardiovascular disease (Supplemental Data, Case ID 452, Quaio et al. 2020. PubMed ID: 33258288) and in an individual with Erdheim-Chester disease (ECD) (Diamond et al. 2019. PubMed ID: 30867592). Functional studies also showed that this variant alters protein function (Diamond et al. 2019. PubMed ID: 30867592). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare, and is reported as pathogenic and likely pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/8274/). This variant is interpreted as pathogenic. - |
Noonan syndrome 1 Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Molecular Genetics, Centre for Human Genetics | - | - - |
Cardio-facio-cutaneous syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2008 | - - |
Noonan syndrome and Noonan-related syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at