5-140786787-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018900.4(PCDHA1):c.497C>A(p.Ala166Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
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.497C>A | p.Ala166Asp | missense_variant | Exon 1 of 4 | ENST00000504120.4 | NP_061723.1 | |
PCDHA1 | NM_031410.2 | c.497C>A | p.Ala166Asp | missense_variant | Exon 1 of 1 | NP_113598.1 | ||
PCDHA1 | NM_031411.3 | c.497C>A | p.Ala166Asp | missense_variant | Exon 1 of 4 | NP_113599.1 | ||
PCDHA@ | n.140786787C>A | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA1 | ENST00000504120.4 | c.497C>A | p.Ala166Asp | missense_variant | Exon 1 of 4 | 1 | NM_018900.4 | ENSP00000420840.3 | ||
PCDHA1 | ENST00000394633.7 | c.497C>A | p.Ala166Asp | missense_variant | Exon 1 of 4 | 1 | ENSP00000378129.3 | |||
PCDHA1 | ENST00000378133.4 | c.497C>A | p.Ala166Asp | missense_variant | Exon 1 of 1 | 6 | ENSP00000367373.3 | |||
ENSG00000279726 | ENST00000655235.1 | n.2725G>T | non_coding_transcript_exon_variant | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152218Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727238
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.497C>A (p.A166D) alteration is located in exon 1 (coding exon 1) of the PCDHA1 gene. This alteration results from a C to A substitution at nucleotide position 497, causing the alanine (A) at amino acid position 166 to be replaced by an aspartic acid (D). 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