12-93678822-GGGTGCAGA-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPP5_Moderate
The NM_003805.5(CRADD):c.52_59del(p.Ala18IlefsTer47) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CRADD
NM_003805.5 frameshift
NM_003805.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.38
Genes affected
CRADD (HGNC:2340): (CASP2 and RIPK1 domain containing adaptor with death domain) This gene encodes a protein containing a death domain (DD) motif. This protein recruits caspase 2/ICH1 to the cell death signal transduction complex, which includes tumor necrosis factor receptor 1 (TNFR1A) and RIPK1/RIP kinase, and acts in promoting apoptosis. A mutation in this gene was associated with cognitive disability. A related pseudogene is found on chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 8 pathogenic variants in the truncated region.
PP5
?
Variant 12-93678822-GGGTGCAGA-G is Pathogenic according to our data. Variant chr12-93678822-GGGTGCAGA-G is described in ClinVar as [Pathogenic]. Clinvar id is 1458241.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRADD | NM_003805.5 | c.52_59del | p.Ala18IlefsTer47 | frameshift_variant | 2/3 | ENST00000332896.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRADD | ENST00000332896.8 | c.52_59del | p.Ala18IlefsTer47 | frameshift_variant | 2/3 | 1 | NM_003805.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
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?
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32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250958Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135714
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000274 AC: 4AN: 1461842Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 727222
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? Cov.: 32
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Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1458241). This premature translational stop signal has been observed in individual(s) with lissencephaly (PMID: 28686357). This variant is present in population databases (rs764518202, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Ala18Ilefs*47) in the CRADD gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CRADD are known to be pathogenic (PMID: 27773430). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at