3-108579413-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3

The NM_020890.3(CIP2A):​c.686G>C​(p.Arg229Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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

Genomes: not found (cov: 32)

Consequence

CIP2A
NM_020890.3 missense

Scores

3
10
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.58

Publications

34 publications found
Variant links:
Genes affected
CIP2A (HGNC:29302): (cellular inhibitor of PP2A) Enables protein homodimerization activity. Predicted to act upstream of or within positive regulation of neural precursor cell proliferation and spermatogenesis. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.821

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CIP2ANM_020890.3 linkc.686G>C p.Arg229Pro missense_variant Exon 7 of 21 ENST00000295746.13 NP_065941.2 Q8TCG1-1
CIP2AXM_006713716.4 linkc.683G>C p.Arg228Pro missense_variant Exon 7 of 21 XP_006713779.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CIP2AENST00000295746.13 linkc.686G>C p.Arg229Pro missense_variant Exon 7 of 21 1 NM_020890.3 ENSP00000295746.7 Q8TCG1-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.89
BayesDel_addAF
Pathogenic
0.22
D
BayesDel_noAF
Uncertain
0.080
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.097
T;.;T
Eigen
Uncertain
0.50
Eigen_PC
Uncertain
0.52
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.89
D;D;D
M_CAP
Benign
0.044
D
MetaRNN
Pathogenic
0.82
D;D;D
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
1.8
L;.;.
PhyloP100
2.6
PrimateAI
Uncertain
0.65
T
PROVEAN
Uncertain
-3.1
D;D;.
REVEL
Benign
0.22
Sift
Uncertain
0.0050
D;D;.
Sift4G
Uncertain
0.013
D;D;D
Polyphen
0.92
P;.;.
Vest4
0.68
MutPred
0.43
Gain of loop (P = 0.0435);.;Gain of loop (P = 0.0435);
MVP
0.71
MPC
0.65
ClinPred
0.98
D
GERP RS
5.1
Varity_R
0.92
gMVP
0.65
Mutation Taster
=31/69
disease causing

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2278911; hg19: chr3-108298260; API