5-141344278-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018916.4(PCDHGA3):c.245G>A(p.Gly82Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000744 in 1,613,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGA3 | NM_018916.4 | c.245G>A | p.Gly82Asp | missense_variant | Exon 1 of 4 | ENST00000253812.8 | NP_061739.2 | |
PCDHGA2 | NM_018915.4 | c.2424+2883G>A | intron_variant | Intron 1 of 3 | ENST00000394576.3 | NP_061738.1 | ||
PCDHGA1 | NM_018912.3 | c.2421+11173G>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.245G>A | p.Gly82Asp | missense_variant | Exon 1 of 4 | 1 | NM_018916.4 | ENSP00000253812.7 | ||
PCDHGA2 | ENST00000394576.3 | c.2424+2883G>A | intron_variant | Intron 1 of 3 | 1 | NM_018915.4 | ENSP00000378077.2 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+11173G>A | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249896Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135550
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461724Hom.: 0 Cov.: 32 AF XY: 0.0000743 AC XY: 54AN XY: 727146
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.245G>A (p.G82D) 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 245, causing the glycine (G) at amino acid position 82 to be replaced by an aspartic acid (D). 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