5-141339330-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018915.4(PCDHGA2):āc.359A>Gā(p.Glu120Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000314 in 1,614,130 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018915.4 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 |
---|---|---|---|---|---|---|---|---|
PCDHGA2 | NM_018915.4 | c.359A>G | p.Glu120Gly | missense_variant | Exon 1 of 4 | ENST00000394576.3 | NP_061738.1 | |
PCDHGA1 | NM_018912.3 | c.2421+6225A>G | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 | ||
PCDHGA2 | NM_032009.3 | c.359A>G | p.Glu120Gly | missense_variant | Exon 1 of 1 | NP_114398.1 | ||
PCDHG@ | n.141339330A>G | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA2 | ENST00000394576.3 | c.359A>G | p.Glu120Gly | missense_variant | Exon 1 of 4 | 1 | NM_018915.4 | ENSP00000378077.2 | ||
PCDHGA1 | ENST00000517417.3 | c.2421+6225A>G | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 | |||
PCDHGA2 | ENST00000528330.2 | c.359A>G | p.Glu120Gly | missense_variant | Exon 1 of 1 | 6 | ENSP00000483020.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251378Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135860
GnomAD4 exome AF: 0.000335 AC: 490AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.000352 AC XY: 256AN XY: 727242
GnomAD4 genome AF: 0.000112 AC: 17AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.359A>G (p.E120G) alteration is located in exon 1 (coding exon 1) of the PCDHGA2 gene. This alteration results from a A to G substitution at nucleotide position 359, causing the glutamic acid (E) at amino acid position 120 to be replaced by a glycine (G). 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