The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_002755.4(MAP2K1):c.370C>T (p.Pro124Ser)

CA16602456

375981 (ClinVar)

Gene: MAP2K1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 5725ca85-ac7d-4884-bdcb-d5ee4a24cee6
Approved on: 2025-01-10
Published on: 2025-09-26

HGVS expressions

NM_002755.4:c.370C>T
NM_002755.4(MAP2K1):c.370C>T (p.Pro124Ser)
NC_000015.10:g.66436824C>T
CM000677.2:g.66436824C>T
NC_000015.9:g.66729162C>T
CM000677.1:g.66729162C>T
NC_000015.8:g.64516216C>T
NG_008305.1:g.54952C>T
ENST00000684779.1:c.304C>T
ENST00000685172.1:c.370C>T
ENST00000685763.1:c.291+1587C>T
ENST00000686347.1:c.370C>T
ENST00000687191.1:n.806C>T
ENST00000689951.1:c.370C>T
ENST00000691077.1:c.370C>T
ENST00000691576.1:c.370C>T
ENST00000691937.1:c.370C>T
ENST00000692487.1:c.370C>T
ENST00000692683.1:c.304C>T
ENST00000693150.1:c.304C>T
ENST00000307102.10:c.370C>T
ENST00000307102.9:c.370C>T
ENST00000425818.2:n.881C>T
NM_002755.3:c.370C>T
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Pathogenic

Met criteria codes 8
PS2_Very Strong PS3_Supporting PM2_Supporting PS4_Moderate PP2 PP3 PM1 PM5
Not Met criteria codes 2
BA1 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MAP2K1 Version 2.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The NM_002755.4:c.370C>T variant in MAP2K1 is a missense variant predicted to cause substitution of proline by serine at amino acid 124 (p.Pro124Ser). This variant was absent from gnomAD v2.1.1 (PM2_Supporting). The computational prediction tool REVEL gives a score of 0.855, suggesting that this variant may impact the protein (PP3). The p.Pro124Ser 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). The variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a critical domain of MAP2K1 (AA 124-134, PM1). Furthermore, 4 different (likely) pathogenic variants at this residue (Pro124Leu, Pro124Arg, Pro124Ala, Pro124Gln) have been identified in several patients with RASopathies (PM5). This variant has been observed in at least 7 probands with a RASopathy, of which 3 were reported as a de novo occurrence with confirmed parental relationships and 1 was assumed to be de novo (PS2_VeryStrong, PS4_Moderate; PMIDs: 36777711, 32978145, GeneDx, LabCorp, ClinVar SCV000572401.6, SCV003316958.3). In vitro functional studies showed that the p.Pro124Ser variant led to ERK1/2 phosphorylation indicating that the mutant was constitutively active (PS3_Supporting; PMID: 22197931). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy Variant Curation Expert Panel: PS2_VeryStrong, PS4_Moderate, PM1, PM5, PS3_Supporting PM2_Supporting, PP2, PP3 (Specification Version 2.3, 1/10/2025)
Met criteria codes
PS2_Very Strong
This variant was observed in 4 de novo cases, of which 3 were with parental confirmation and 1 was assumed de novo.
PS3_Supporting
Compared to WT MAP2K1, the P124S variant caused increased phosphorylation of ERK1/2 in HEK293T cells. BRAFV600E was used as a positive control.
PM2_Supporting
This variant is absent from gnomAD v2.1.1
PS4_Moderate
This variant has been observed in at least 7 probands with a RASopathy (PMIDs: 36777711, 32978145, GeneDx, LabCorp, ClinVar SCV000572401.6, SCV003316958.3).
PP2
MAP2K1 is a missense-constrained gene. The gnomAD Z-score for missense variants in the gene is 3.76.
PP3
The REVEL score is 0.855 and the variant is entirely conserved in UCSC database.
PM1
It falls between amino acids 124 and 134 which is a critical functional domain.
PM5
There were four other P/LP variants at this residue (P124L, P124R, P124A, P124Q), however PM3 was capped at moderate strength when applied in conjunction with PM1
Not Met criteria codes
BA1
This variant is absent from gnomAD v2.1.1
BS1
This variant is absent from gnomAD v2.1.1
Curation History
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