12-94308820-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_016122.3(CEP83):​c.2099G>A​(p.Gly700Glu) 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. 13/20 in silico tools predict a benign 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. G700R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

CEP83
NM_016122.3 missense

Scores

5
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.68
Variant links:
Genes affected
CEP83 (HGNC:17966): (centrosomal protein 83) The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37105814).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CEP83NM_016122.3 linkc.2099G>A p.Gly700Glu missense_variant Exon 17 of 17 ENST00000397809.10 NP_057206.2 Q9Y592-1Q3B787

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CEP83ENST00000397809.10 linkc.2099G>A p.Gly700Glu missense_variant Exon 17 of 17 1 NM_016122.3 ENSP00000380911.4 Q9Y592-1
CEP83ENST00000339839.9 linkc.2099G>A p.Gly700Glu missense_variant Exon 16 of 16 1 ENSP00000344655.5 Q9Y592-1
CEP83ENST00000552632.5 linkc.491G>A p.Gly164Glu missense_variant Exon 4 of 5 3 ENSP00000447094.1 H0YHH5
CEP83ENST00000546783.1 linkn.*7G>A downstream_gene_variant 3

Frequencies

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

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Nephronophthisis 18 Uncertain:1
Nov 11, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 700 of the CEP83 protein (p.Gly700Glu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CEP83-related conditions. ClinVar contains an entry for this variant (Variation ID: 1059602). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.057
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
20
DANN
Uncertain
0.99
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.51
T;.;T
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.37
T;T;T
MetaSVM
Benign
-0.85
T
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-1.8
N;N;N
REVEL
Benign
0.16
Sift
Uncertain
0.020
D;D;D
Sift4G
Benign
0.13
T;T;T
Vest4
0.27, 0.28
MVP
0.69
MPC
0.50
ClinPred
0.71
D
GERP RS
5.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.056
gMVP
0.19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-94702596; API