2-171443558-CA-CAA
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_025000.4(DCAF17):c.270dup(p.Cys91MetfsTer28) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
DCAF17
NM_025000.4 frameshift
NM_025000.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.07
Genes affected
DCAF17 (HGNC:25784): (DDB1 and CUL4 associated factor 17) This gene encodes a nuclear transmembrane protein that associates with cullin 4A/damaged DNA binding protein 1 ubiquitin ligase complex. Mutations in this gene are associated with Woodhouse-Sakati syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-171443558-C-CA is Pathogenic according to our data. Variant chr2-171443558-C-CA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 632550.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCAF17 | NM_025000.4 | c.270dup | p.Cys91MetfsTer28 | frameshift_variant | 3/14 | ENST00000375255.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCAF17 | ENST00000375255.8 | c.270dup | p.Cys91MetfsTer28 | frameshift_variant | 3/14 | 1 | NM_025000.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Woodhouse-Sakati syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Hacettepe Genetic Diseases Diagnosis Center, Hacettepe University Faculty of Medicine | Dec 06, 2017 | Sequencing analysis revealed a novel frameshift mutation NM_025000.4: c.270dup (p.Cys91Metfs*28) in exon 3 of DCAF17 in patient with hyper-hypogonadotropic hypogonadism, non-autoimmune insulinopenic diabetes mellitus and pituitary MRI indicated paramagnetic substance deposition in gland. These clinical findings and molecular results consistent with Woodhouse-Sakati Syndrome. Parents were found to be heterozygous carriers of this mutation. This variant was not reported in ExAC and gnomAD databases and was evaluated as pathogenic by in silico analysis such as MutationTaster. - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at