5-141339174-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018915.4(PCDHGA2):c.203C>A(p.Ser68Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
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.203C>A | p.Ser68Tyr | missense_variant | Exon 1 of 4 | ENST00000394576.3 | NP_061738.1 | |
PCDHGA1 | NM_018912.3 | c.2421+6069C>A | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 | ||
PCDHGA2 | NM_032009.3 | c.203C>A | p.Ser68Tyr | missense_variant | Exon 1 of 1 | NP_114398.1 | ||
PCDHG@ | n.141339174C>A | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA2 | ENST00000394576.3 | c.203C>A | p.Ser68Tyr | missense_variant | Exon 1 of 4 | 1 | NM_018915.4 | ENSP00000378077.2 | ||
PCDHGA1 | ENST00000517417.3 | c.2421+6069C>A | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 | |||
PCDHGA2 | ENST00000528330.2 | c.203C>A | p.Ser68Tyr | missense_variant | Exon 1 of 1 | 6 | ENSP00000483020.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461770Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727160
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.203C>A (p.S68Y) alteration is located in exon 1 (coding exon 1) of the PCDHGA2 gene. This alteration results from a C to A substitution at nucleotide position 203, causing the serine (S) at amino acid position 68 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.