2-204686184-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001302769.2(PARD3B):​c.124C>G​(p.Pro42Ala) 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 benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P42T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

PARD3B
NM_001302769.2 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.82

Publications

0 publications found
Variant links:
Genes affected
PARD3B (HGNC:14446): (par-3 family cell polarity regulator beta) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in several processes, including establishment of cell polarity; establishment of centrosome localization; and establishment or maintenance of epithelial cell apical/basal polarity. Located in cell junction. Part of protein-containing complex. [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 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.35755533).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PARD3BNM_001302769.2 linkc.124C>G p.Pro42Ala missense_variant Exon 2 of 23 ENST00000406610.7 NP_001289698.1 Q8TEW8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PARD3BENST00000406610.7 linkc.124C>G p.Pro42Ala missense_variant Exon 2 of 23 1 NM_001302769.2 ENSP00000385848.2 Q8TEW8-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
28
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.068
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.043
T;T;.;.;.
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.50
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Benign
0.74
T;T;T;T;T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.36
T;T;T;T;T
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
1.3
L;.;L;L;L
PhyloP100
2.8
PrimateAI
Uncertain
0.62
T
PROVEAN
Pathogenic
-5.1
D;.;D;D;D
REVEL
Benign
0.21
Sift
Benign
0.034
D;.;D;T;D
Sift4G
Benign
0.23
T;T;T;T;T
Polyphen
1.0
D;.;P;.;D
Vest4
0.36
MutPred
0.35
Gain of catalytic residue at P42 (P = 0.0118);Gain of catalytic residue at P42 (P = 0.0118);Gain of catalytic residue at P42 (P = 0.0118);Gain of catalytic residue at P42 (P = 0.0118);Gain of catalytic residue at P42 (P = 0.0118);
MVP
0.79
MPC
0.072
ClinPred
0.99
D
GERP RS
5.1
Varity_R
0.24
gMVP
0.13
Mutation Taster
=94/6
polymorphism

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: rs1470103462; hg19: chr2-205550907; API