rs747119727
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_058004.4(PI4KA):āc.5560G>Cā(p.Asp1854His) variant causes a missense change. The variant allele was found at a frequency of 0.0000014 in 1,431,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. D1854N) has been classified as Likely pathogenic.
Frequency
Consequence
NM_058004.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PI4KA | NM_058004.4 | c.5560G>C | p.Asp1854His | missense_variant | 48/55 | ENST00000255882.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PI4KA | ENST00000255882.11 | c.5560G>C | p.Asp1854His | missense_variant | 48/55 | 1 | NM_058004.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1431728Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 2AN XY: 709682
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at