rs1557135441
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM4
The NM_001110792.2(MECP2):c.1159_1227del(p.Ser387_Glu409del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000000915 in 1,093,222 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S387S) has been classified as Likely benign.
Frequency
Consequence
NM_001110792.2 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.1159_1227del | p.Ser387_Glu409del | inframe_deletion | 3/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.1123_1191del | p.Ser375_Glu397del | inframe_deletion | 4/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000303391.11 | c.1123_1191del | p.Ser375_Glu397del | inframe_deletion | 4/4 | 1 | NM_004992.4 | P1 | |
MECP2 | ENST00000453960.7 | c.1159_1227del | p.Ser387_Glu409del | inframe_deletion | 3/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000407218.5 | c.*495_*563del | 3_prime_UTR_variant | 4/4 | 5 | ||||
MECP2 | ENST00000628176.2 | c.*495_*563del | 3_prime_UTR_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 17
GnomAD4 exome AF: 9.15e-7 AC: 1AN: 1093222Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 360664
GnomAD4 genome ? Cov.: 17
ClinVar
Submissions by phenotype
Rett syndrome Uncertain:2
Uncertain significance, no assertion criteria provided | curation | RettBASE | Apr 10, 2002 | - - |
Uncertain significance, criteria provided, single submitter | curation | Centre for Population Genomics, CPG | Jan 12, 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 3.0, this variant is classified as a variant of uncertain significance. At least the following criteria are met: The variant is observed in at least 1 individual with no features of Rett Syndrome (BS2_Supporting) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at