19-36100749-CAGAG-CAG
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1PM2PP3PP5_Very_Strong
The NM_001083961.2(WDR62):c.2746_2747delAG(p.Gln918GlyfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,888 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001083961.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250830Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135624
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461684Hom.: 0 AF XY: 0.00000688 AC XY: 5AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
Microcephaly 2, primary, autosomal recessive, with or without cortical malformations Pathogenic:3
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The p.Gln918GlyfsX18 variant WDR62 has been reported in 2 siblings with autosomal recessive microcephaly/polymicrogyria in a compound heterozygous state with another frameshift variant (Murdock 2011 PMID: 21834044). It was also identified in 1/113224 of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 918 and leads to a premature termination codon 18 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the WDR62 gene is strongly associated with autosomal recessive primary microcephaly/polymicrogyria. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive primary microcephaly. ACMG/AMP Criteria applied: PM2, PVS1, PP1, PM3. -
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not provided Pathogenic:1
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21834044) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at