rs782739980
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018908.3(PCDHA5):c.137G>T(p.Arg46Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018908.3 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 |
---|---|---|---|---|---|---|---|---|
PCDHA5 | NM_018908.3 | c.137G>T | p.Arg46Leu | missense_variant | Exon 1 of 4 | ENST00000529859.2 | NP_061731.1 | |
PCDHA1 | NM_018900.4 | c.2394+33228G>T | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA3 | NM_018906.3 | c.2394+18321G>T | intron_variant | Intron 1 of 3 | ENST00000522353.3 | NP_061729.1 | ||
PCDHA2 | NM_018905.3 | c.2388+24560G>T | intron_variant | Intron 1 of 3 | ENST00000526136.2 | NP_061728.1 | ||
PCDHA4 | NM_018907.4 | c.2385+12340G>T | intron_variant | Intron 1 of 3 | ENST00000530339.2 | NP_061730.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA5 | ENST00000529859.2 | c.137G>T | p.Arg46Leu | missense_variant | Exon 1 of 4 | 1 | NM_018908.3 | ENSP00000436557.1 | ||
PCDHA1 | ENST00000504120.4 | c.2394+33228G>T | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA3 | ENST00000522353.3 | c.2394+18321G>T | intron_variant | Intron 1 of 3 | 1 | NM_018906.3 | ENSP00000429808.2 | |||
PCDHA2 | ENST00000526136.2 | c.2388+24560G>T | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 | |||
PCDHA4 | ENST00000530339.2 | c.2385+12340G>T | intron_variant | Intron 1 of 3 | 1 | NM_018907.4 | ENSP00000435300.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251330Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135880
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461844Hom.: 0 Cov.: 35 AF XY: 0.0000440 AC XY: 32AN XY: 727230
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.137G>T (p.R46L) alteration is located in exon 1 (coding exon 1) of the PCDHA5 gene. This alteration results from a G to T substitution at nucleotide position 137, causing the arginine (R) at amino acid position 46 to be replaced by a leucine (L). 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