rs200854927
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001184880.2(PCDH19):c.3235C>T(p.Pro1079Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000165 in 1,209,209 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1079A) has been classified as Likely benign.
Frequency
Consequence
NM_001184880.2 missense
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 |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.3235C>T | p.Pro1079Ser | missense_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.3094C>T | p.Pro1032Ser | missense_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.3091C>T | p.Pro1031Ser | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.3235C>T | p.Pro1079Ser | missense_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.3094C>T | p.Pro1032Ser | missense_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.3091C>T | p.Pro1031Ser | missense_variant | 5/5 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000899 AC: 1AN: 111187Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33365
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098022Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 363378
GnomAD4 genome ? AF: 0.00000899 AC: 1AN: 111187Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33365
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at