5-140786424-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018900.4(PCDHA1):āc.134T>Cā(p.Val45Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,460 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018900.4 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 |
---|---|---|---|---|---|---|---|---|
PCDHA1 | NM_018900.4 | c.134T>C | p.Val45Ala | missense_variant | Exon 1 of 4 | ENST00000504120.4 | NP_061723.1 | |
PCDHA1 | NM_031410.2 | c.134T>C | p.Val45Ala | missense_variant | Exon 1 of 1 | NP_113598.1 | ||
PCDHA1 | NM_031411.3 | c.134T>C | p.Val45Ala | missense_variant | Exon 1 of 4 | NP_113599.1 | ||
PCDHA@ | n.140786424T>C | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA1 | ENST00000504120.4 | c.134T>C | p.Val45Ala | missense_variant | Exon 1 of 4 | 1 | NM_018900.4 | ENSP00000420840.3 | ||
PCDHA1 | ENST00000394633.7 | c.134T>C | p.Val45Ala | missense_variant | Exon 1 of 4 | 1 | ENSP00000378129.3 | |||
PCDHA1 | ENST00000378133.4 | c.134T>C | p.Val45Ala | missense_variant | Exon 1 of 1 | 6 | ENSP00000367373.3 | |||
ENSG00000279726 | ENST00000655235.1 | n.3088A>G | non_coding_transcript_exon_variant | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251382Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135896
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461098Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726866
GnomAD4 genome AF: 0.000138 AC: 21AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.134T>C (p.V45A) alteration is located in exon 1 (coding exon 1) of the PCDHA1 gene. This alteration results from a T to C substitution at nucleotide position 134, causing the valine (V) at amino acid position 45 to be replaced by an alanine (A). 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