NM_025000.4:c.270delA
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_025000.4(DCAF17):c.270delA(p.Lys90AsnfsTer8) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,764 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
DCAF17
NM_025000.4 frameshift
NM_025000.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.07
Publications
3 publications found
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]
DCAF17 Gene-Disease associations (from GenCC):
- Woodhouse-Sakati syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Genomics England PanelApp, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 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-CA-C is Pathogenic according to our data. Variant chr2-171443558-CA-C is described in ClinVar as Pathogenic. ClinVar VariationId is 212711.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_025000.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DCAF17 | MANE Select | c.270delA | p.Lys90AsnfsTer8 | frameshift | Exon 3 of 14 | NP_079276.2 | Q5H9S7-1 | ||
| DCAF17 | c.270delA | p.Lys90AsnfsTer8 | frameshift | Exon 3 of 12 | NP_001158293.1 | F5H7W1 | |||
| DCAF17 | n.622delA | non_coding_transcript_exon | Exon 3 of 13 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DCAF17 | TSL:1 MANE Select | c.270delA | p.Lys90AsnfsTer8 | frameshift | Exon 3 of 14 | ENSP00000364404.3 | Q5H9S7-1 | ||
| DCAF17 | c.270delA | p.Lys90AsnfsTer8 | frameshift | Exon 3 of 15 | ENSP00000636727.1 | ||||
| DCAF17 | c.261delA | p.Lys87AsnfsTer8 | frameshift | Exon 3 of 14 | ENSP00000577692.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000401 AC: 1AN: 249246 AF XY: 0.00000739 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
249246
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460764Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726738 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1460764
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
726738
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33452
American (AMR)
AF:
AC:
0
AN:
44706
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26096
East Asian (EAS)
AF:
AC:
0
AN:
39498
South Asian (SAS)
AF:
AC:
1
AN:
86222
European-Finnish (FIN)
AF:
AC:
0
AN:
53256
Middle Eastern (MID)
AF:
AC:
0
AN:
5752
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111434
Other (OTH)
AF:
AC:
0
AN:
60348
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
1
-
-
Woodhouse-Sakati syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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