X-100407808-C-G
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_001184880.2(PCDH19):c.790G>C(p.Asp264His) 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. D264Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001184880.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.790G>C | p.Asp264His | missense_variant | Exon 1 of 6 | ENST00000373034.8 | NP_001171809.1 | |
PCDH19 | NM_001105243.2 | c.790G>C | p.Asp264His | missense_variant | Exon 1 of 5 | NP_001098713.1 | ||
PCDH19 | NM_020766.3 | c.790G>C | p.Asp264His | missense_variant | Exon 1 of 5 | NP_065817.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.790G>C | p.Asp264His | missense_variant | Exon 1 of 6 | 1 | NM_001184880.2 | ENSP00000362125.4 | ||
PCDH19 | ENST00000255531.8 | c.790G>C | p.Asp264His | missense_variant | Exon 1 of 5 | 1 | ENSP00000255531.7 | |||
PCDH19 | ENST00000420881.6 | c.790G>C | p.Asp264His | missense_variant | Exon 1 of 5 | 1 | ENSP00000400327.2 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Intellectual disability Pathogenic:1
- -
Developmental and epileptic encephalopathy, 9 Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at