NM_018908.3:c.272G>T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018908.3(PCDHA5):c.272G>T(p.Arg91Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHA5 | NM_018908.3 | c.272G>T | p.Arg91Leu | missense_variant | Exon 1 of 4 | ENST00000529859.2 | NP_061731.1 | |
PCDHA1 | NM_018900.4 | c.2394+33363G>T | intron_variant | Intron 1 of 3 | ENST00000504120.4 | NP_061723.1 | ||
PCDHA3 | NM_018906.3 | c.2394+18456G>T | intron_variant | Intron 1 of 3 | ENST00000522353.3 | NP_061729.1 | ||
PCDHA2 | NM_018905.3 | c.2388+24695G>T | intron_variant | Intron 1 of 3 | ENST00000526136.2 | NP_061728.1 | ||
PCDHA4 | NM_018907.4 | c.2385+12475G>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.272G>T | p.Arg91Leu | missense_variant | Exon 1 of 4 | 1 | NM_018908.3 | ENSP00000436557.1 | ||
PCDHA1 | ENST00000504120.4 | c.2394+33363G>T | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 | |||
PCDHA3 | ENST00000522353.3 | c.2394+18456G>T | intron_variant | Intron 1 of 3 | 1 | NM_018906.3 | ENSP00000429808.2 | |||
PCDHA2 | ENST00000526136.2 | c.2388+24695G>T | intron_variant | Intron 1 of 3 | 1 | NM_018905.3 | ENSP00000431748.1 | |||
PCDHA4 | ENST00000530339.2 | c.2385+12475G>T | intron_variant | Intron 1 of 3 | 1 | NM_018907.4 | ENSP00000435300.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.272G>T (p.R91L) 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 272, causing the arginine (R) at amino acid position 91 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