The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_002755.3(MAP2K1):c.169A>C (p.Lys57Gln)

CA134595

40779 (ClinVar)

Gene: MAP2K1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 5fa3b275-1dad-4c57-bed5-dd904a8b11bb

HGVS expressions

NM_002755.3:c.169A>C
NM_002755.3(MAP2K1):c.169A>C (p.Lys57Gln)
NM_002755.4:c.169A>C
ENST00000307102.9:c.169A>C
ENST00000425818.2:n.680A>C
NC_000015.10:g.66435115A>C
CM000677.2:g.66435115A>C
NC_000015.9:g.66727453A>C
CM000677.1:g.66727453A>C
NC_000015.8:g.64514507A>C
NG_008305.1:g.53243A>C

Pathogenic

Met criteria codes 7
PS2 PP3 PP2 PM1 PM6 PM2 PS4_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.169A>C (p.Lys57Gln) variant in MAP2K1 was absent from large population studies (PM2; gnomAD.broadinstitute.org). It has been reported in 3 total patients with clinical features of a RASopathy (PS4_Moderate; SCV000061249.5; Otto von Guericke University Magdeburg internal data; Invitae internal data). One was a confirmed de novo occurrence and one was an unconfirmed de novo occurrence (PS2; PM6; SCV000061249.5; Otto von Guericke University Magdeburg internal data). The p.Lys57Gln variant is located in the negative regulatory region, which has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K1 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Lys57Gln variant may impact the protein (PP3). Furthermore, the variant is located in MAP2K1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2, PS4_Moderate, PM2, PM6, PM1, PP3, PP2.
Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
Computational prediction tools and conservation analysis suggest that the p.Lys57Gln variant may impact the protein (PP3)
PP2
The variant is located in the MAP2K1 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).
PM1
Negative regulatory region
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4_Moderate
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2020-06-25
Published on: 2020-06-25
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.