5-141339479-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018915.4(PCDHGA2):āc.508T>Cā(p.Tyr170His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,614,008 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 (ā ).
Frequency
Consequence
NM_018915.4 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 |
---|---|---|---|---|---|---|---|---|
PCDHGA2 | NM_018915.4 | c.508T>C | p.Tyr170His | missense_variant | Exon 1 of 4 | ENST00000394576.3 | NP_061738.1 | |
PCDHGA1 | NM_018912.3 | c.2421+6374T>C | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 | ||
PCDHGA2 | NM_032009.3 | c.508T>C | p.Tyr170His | missense_variant | Exon 1 of 1 | NP_114398.1 | ||
PCDHG@ | n.141339479T>C | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA2 | ENST00000394576.3 | c.508T>C | p.Tyr170His | missense_variant | Exon 1 of 4 | 1 | NM_018915.4 | ENSP00000378077.2 | ||
PCDHGA1 | ENST00000517417.3 | c.2421+6374T>C | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 | |||
PCDHGA2 | ENST00000528330.2 | c.508T>C | p.Tyr170His | missense_variant | Exon 1 of 1 | 6 | ENSP00000483020.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251492Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135920
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461882Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.508T>C (p.Y170H) alteration is located in exon 1 (coding exon 1) of the PCDHGA2 gene. This alteration results from a T to C substitution at nucleotide position 508, causing the tyrosine (Y) at amino acid position 170 to be replaced by a histidine (H). 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