X-154030539-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_001110792.2(MECP2):c.1325C>T(p.Pro442Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000108 in 1,208,933 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P442S) has been classified as Benign.
Frequency
Consequence
NM_001110792.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.1325C>T | p.Pro442Leu | missense_variant | 3/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.1289C>T | p.Pro430Leu | missense_variant | 4/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000453960.7 | c.1325C>T | p.Pro442Leu | missense_variant | 3/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000303391.11 | c.1289C>T | p.Pro430Leu | missense_variant | 4/4 | 1 | NM_004992.4 | P1 | |
MECP2 | ENST00000628176.2 | c.*661C>T | 3_prime_UTR_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000180 AC: 2AN: 111075Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33279
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182941Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67451
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1097858Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 6AN XY: 363262
GnomAD4 genome AF: 0.0000180 AC: 2AN: 111075Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33279
ClinVar
Submissions by phenotype
Severe neonatal-onset encephalopathy with microcephaly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at