rs1192424800
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP2PP3_Moderate
The NM_002739.5(PRKCG):c.412G>A(p.Val138Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000698 in 1,432,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V138E) has been classified as Pathogenic.
Frequency
Consequence
NM_002739.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCG | NM_002739.5 | c.412G>A | p.Val138Met | missense_variant | 5/18 | ENST00000263431.4 | |
PRKCG | NM_001316329.2 | c.412G>A | p.Val138Met | missense_variant | 5/19 | ||
PRKCG | XM_047439092.1 | c.28G>A | p.Val10Met | missense_variant | 6/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCG | ENST00000263431.4 | c.412G>A | p.Val138Met | missense_variant | 5/18 | 1 | NM_002739.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000507 AC: 1AN: 197310Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 107442
GnomAD4 exome AF: 6.98e-7 AC: 1AN: 1432690Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 710072
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at