NM_018916.4:c.259G>C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018916.4(PCDHGA3):āc.259G>Cā(p.Ala87Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,740 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018916.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGA3 | NM_018916.4 | c.259G>C | p.Ala87Pro | missense_variant | Exon 1 of 4 | ENST00000253812.8 | NP_061739.2 | |
PCDHGA2 | NM_018915.4 | c.2424+2897G>C | intron_variant | Intron 1 of 3 | ENST00000394576.3 | NP_061738.1 | ||
PCDHGA1 | NM_018912.3 | c.2421+11187G>C | 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.259G>C | p.Ala87Pro | missense_variant | Exon 1 of 4 | 1 | NM_018916.4 | ENSP00000253812.7 | ||
PCDHGA2 | ENST00000394576.3 | c.2424+2897G>C | intron_variant | Intron 1 of 3 | 1 | NM_018915.4 | ENSP00000378077.2 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+11187G>C | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249800Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135522
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461740Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727152
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.259G>C (p.A87P) alteration is located in exon 1 (coding exon 1) of the PCDHGA3 gene. This alteration results from a G to C substitution at nucleotide position 259, causing the alanine (A) at amino acid position 87 to be replaced by a proline (P). 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