rs144233940
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000401500.7(WDR62):āc.3368A>Cā(p.Gln1123Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,952 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1123R) has been classified as Likely benign.
Frequency
Consequence
ENST00000401500.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR62 | NM_001083961.2 | c.3368A>C | p.Gln1123Pro | missense_variant | 28/32 | ENST00000401500.7 | NP_001077430.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR62 | ENST00000401500.7 | c.3368A>C | p.Gln1123Pro | missense_variant | 28/32 | 1 | NM_001083961.2 | ENSP00000384792 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250978Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135752
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461798Hom.: 1 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727196
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 31, 2023 | This sequence change replaces glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 1123 of the WDR62 protein (p.Gln1123Pro). This variant is present in population databases (rs144233940, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with WDR62-related conditions. ClinVar contains an entry for this variant (Variation ID: 586941). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt WDR62 protein function. 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 20, 2018 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.3368A>C (p.Q1123P) alteration is located in exon 28 (coding exon 28) of the WDR62 gene. This alteration results from a A to C substitution at nucleotide position 3368, causing the glutamine (Q) at amino acid position 1123 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at