chr16-12781296-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_018340.3(CPPED1):c.178G>A(p.Glu60Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0008 in 1,614,118 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00045 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00084 ( 3 hom. )
Consequence
CPPED1
NM_018340.3 missense
NM_018340.3 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 7.47
Genes affected
CPPED1 (HGNC:25632): (calcineurin like phosphoesterase domain containing 1) Predicted to enable metal ion binding activity; protein serine phosphatase activity; and protein threonine phosphatase activity. Predicted to be involved in protein dephosphorylation. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.32666653).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPPED1 | NM_018340.3 | c.178G>A | p.Glu60Lys | missense_variant | 2/4 | ENST00000381774.9 | |
CPPED1 | NM_001099455.2 | c.178G>A | p.Glu60Lys | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPPED1 | ENST00000381774.9 | c.178G>A | p.Glu60Lys | missense_variant | 2/4 | 1 | NM_018340.3 | P1 | |
CPPED1 | ENST00000433677.6 | c.178G>A | p.Glu60Lys | missense_variant | 2/3 | 1 | |||
CPPED1 | ENST00000261660.4 | c.178G>A | p.Glu60Lys | missense_variant | 2/3 | 2 | |||
CPPED1 | ENST00000539677.1 | n.246G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000454 AC: 69AN: 152132Hom.: 0 Cov.: 32
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?
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GnomAD3 exomes AF: 0.000413 AC: 103AN: 249494Hom.: 0 AF XY: 0.000421 AC XY: 57AN XY: 135364
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GnomAD4 exome AF: 0.000836 AC: 1222AN: 1461868Hom.: 3 Cov.: 31 AF XY: 0.000806 AC XY: 586AN XY: 727230
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GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74444
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.178G>A (p.E60K) alteration is located in exon 2 (coding exon 2) of the CPPED1 gene. This alteration results from a G to A substitution at nucleotide position 178, causing the glutamic acid (E) at amino acid position 60 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at