rs727504353
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_030662.4(MAP2K2):c.985C>T(p.Pro329Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,551,244 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predict no significant impact on normal splicing. 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. P329L) has been classified as Uncertain significance.
Frequency
Consequence
NM_030662.4 missense, splice_region
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.985C>T | p.Pro329Ser | missense_variant, splice_region_variant | 9/11 | ENST00000262948.10 | |
MAP2K2 | XM_006722799.3 | c.706C>T | p.Pro236Ser | missense_variant, splice_region_variant | 7/9 | ||
MAP2K2 | XM_047439100.1 | c.415C>T | p.Pro139Ser | missense_variant, splice_region_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K2 | ENST00000262948.10 | c.985C>T | p.Pro329Ser | missense_variant, splice_region_variant | 9/11 | 1 | NM_030662.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000192 AC: 3AN: 156322Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 82228
GnomAD4 exome AF: 0.0000186 AC: 26AN: 1398944Hom.: 0 Cov.: 30 AF XY: 0.0000101 AC XY: 7AN XY: 690004
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 23, 2013 | The Pro329Ser variant in MEK2 has not been reported in the literature nor previo usly identified by our laboratory. In addition, this variant has not been identi fied in large, ethnically-distinct populations. Computational analyses (biochemi cal amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) do not provide strong support for or against an impact to the protein. In summary, addi tional information is needed to fully assess the clinical significance of the Pr o329Ser variant. - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 01, 2023 | The p.P329S variant (also known as c.985C>T) is located in coding exon 9 of the MAP2K2 gene. The proline at codon 329 is replaced by serine, an amino acid with similar properties. This change occurs in the first base pair of coding exon 9. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at