5-141344299-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018916.4(PCDHGA3):c.266G>A(p.Arg89Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000958 in 1,461,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018916.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGA3 | NM_018916.4 | c.266G>A | p.Arg89Lys | missense_variant | Exon 1 of 4 | ENST00000253812.8 | NP_061739.2 | |
PCDHGA2 | NM_018915.4 | c.2424+2904G>A | intron_variant | Intron 1 of 3 | ENST00000394576.3 | NP_061738.1 | ||
PCDHGA1 | NM_018912.3 | c.2421+11194G>A | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA3 | ENST00000253812.8 | c.266G>A | p.Arg89Lys | missense_variant | Exon 1 of 4 | 1 | NM_018916.4 | ENSP00000253812.7 | ||
PCDHGA2 | ENST00000394576.3 | c.2424+2904G>A | intron_variant | Intron 1 of 3 | 1 | NM_018915.4 | ENSP00000378077.2 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+11194G>A | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249770Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135504
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461732Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727146
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.266G>A (p.R89K) alteration is located in exon 1 (coding exon 1) of the PCDHGA3 gene. This alteration results from a G to A substitution at nucleotide position 266, causing the arginine (R) at amino acid position 89 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at