16-12664975-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018340.3(CPPED1):c.856G>A(p.Glu286Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000819 in 1,610,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018340.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPPED1 | ENST00000381774.9 | c.856G>A | p.Glu286Lys | missense_variant | Exon 4 of 4 | 1 | NM_018340.3 | ENSP00000371193.4 | ||
CPPED1 | ENST00000433677.6 | c.430G>A | p.Glu144Lys | missense_variant | Exon 3 of 3 | 1 | ENSP00000411127.2 | |||
CPPED1 | ENST00000261660.4 | c.335G>A | p.Arg112Gln | missense_variant | Exon 3 of 3 | 2 | ENSP00000261660.4 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000812 AC: 20AN: 246422Hom.: 0 AF XY: 0.0000971 AC XY: 13AN XY: 133934
GnomAD4 exome AF: 0.0000843 AC: 123AN: 1458890Hom.: 0 Cov.: 34 AF XY: 0.0000854 AC XY: 62AN XY: 725856
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.856G>A (p.E286K) alteration is located in exon 4 (coding exon 4) of the CPPED1 gene. This alteration results from a G to A substitution at nucleotide position 856, causing the glutamic acid (E) at amino acid position 286 to be replaced by a lysine (K). 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