rs377253487
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004204.5(PIGQ):c.476C>A(p.Thr159Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000551 in 1,452,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. T159M) has been classified as Uncertain significance.
Frequency
Consequence
NM_004204.5 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 |
---|---|---|---|---|---|---|---|
PIGQ | NM_004204.5 | c.476C>A | p.Thr159Lys | missense_variant | 2/11 | ENST00000321878.10 | |
PIGQ | NM_148920.4 | c.476C>A | p.Thr159Lys | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGQ | ENST00000321878.10 | c.476C>A | p.Thr159Lys | missense_variant | 2/11 | 1 | NM_004204.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000443 AC: 1AN: 225892Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 123810
GnomAD4 exome AF: 0.00000551 AC: 8AN: 1452202Hom.: 0 Cov.: 39 AF XY: 0.00000554 AC XY: 4AN XY: 721646
GnomAD4 genome Cov.: 34
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at