NM_000281.4:c.263G>C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000281.4(PCBD1):āc.263G>Cā(p.Arg88Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000281.4 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 |
---|---|---|---|---|---|---|---|---|
PCBD1 | NM_000281.4 | c.263G>C | p.Arg88Pro | missense_variant | Exon 4 of 4 | ENST00000299299.4 | NP_000272.1 | |
PCBD1 | NM_001289797.2 | c.116G>C | p.Arg39Pro | missense_variant | Exon 4 of 4 | NP_001276726.1 | ||
PCBD1 | NM_001323004.2 | c.216+1150G>C | intron_variant | Intron 3 of 3 | NP_001309933.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251258Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135802
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461826Hom.: 0 Cov.: 35 AF XY: 0.00000688 AC XY: 5AN XY: 727206
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at