X-154031428-A-G
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_001110792.2(MECP2):c.436T>C(p.Ser146Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S146F) has been classified as Pathogenic.
Frequency
Consequence
NM_001110792.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.436T>C | p.Ser146Pro | missense_variant | 3/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.400T>C | p.Ser134Pro | missense_variant | 4/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000453960.7 | c.436T>C | p.Ser146Pro | missense_variant | 3/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000303391.11 | c.400T>C | p.Ser134Pro | missense_variant | 4/4 | 1 | NM_004992.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Rett syndrome Pathogenic:1Uncertain:1
Uncertain significance, no assertion criteria provided | curation | RettBASE | Aug 24, 2010 | - - |
Likely pathogenic, criteria provided, single submitter | curation | Centre for Population Genomics, CPG | Mar 26, 2024 | This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria. Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0, this variant is classified as likely pathogenic. At least the following criteria are met: Occurs in the well-characterized Methyl-DNA binding (MDB) functional domain of MECP2 (PM1). Another missense variant in the same codon has been classified as pathogenic for Rett syndrome (PM5, PMID: 27356039, PMID: 23696494, PMID: 26418480). Computational prediction analysis tools suggests a deleterious impact (REVEL score ‚ > 0.75) (PP3). This variant is absent from gnomAD v4.0.0 (PM2_Supporting). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at