12-94308899-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016122.3(CEP83):c.2020G>A(p.Glu674Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000686 in 1,458,538 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016122.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP83 | ENST00000397809.10 | c.2020G>A | p.Glu674Lys | missense_variant | Exon 17 of 17 | 1 | NM_016122.3 | ENSP00000380911.4 | ||
CEP83 | ENST00000339839.9 | c.2020G>A | p.Glu674Lys | missense_variant | Exon 16 of 16 | 1 | ENSP00000344655.5 | |||
CEP83 | ENST00000552632.5 | c.412G>A | p.Glu138Lys | missense_variant | Exon 4 of 5 | 3 | ENSP00000447094.1 | |||
CEP83 | ENST00000546783.1 | n.474G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458538Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 725758
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nephronophthisis 18 Uncertain:1
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 674 of the CEP83 protein (p.Glu674Lys). 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: 954930). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at