rs797045947
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_006642.5(SDCCAG8):c.481C>T(p.Gln161Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000248 in 1,613,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SDCCAG8
NM_006642.5 stop_gained
NM_006642.5 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 4.79
Genes affected
SDCCAG8 (HGNC:10671): (SHH signaling and ciliogenesis regulator SDCCAG8) This gene encodes a centrosome associated protein. This protein may be involved in organizing the centrosome during interphase and mitosis. Mutations in this gene are associated with retinal-renal ciliopathy. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 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
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Variant 1-243286332-C-T is Pathogenic according to our data. Variant chr1-243286332-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 212140.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDCCAG8 | NM_006642.5 | c.481C>T | p.Gln161Ter | stop_gained | 5/18 | ENST00000366541.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDCCAG8 | ENST00000366541.8 | c.481C>T | p.Gln161Ter | stop_gained | 5/18 | 1 | NM_006642.5 | P1 | |
SDCCAG8 | ENST00000482234.1 | n.214C>T | non_coding_transcript_exon_variant | 3/6 | 3 | ||||
SDCCAG8 | ENST00000490065.5 | n.634C>T | non_coding_transcript_exon_variant | 5/5 | 4 | ||||
SDCCAG8 | ENST00000476722.6 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251240Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135804
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461500Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727064
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SDCCAG8-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 17, 2024 | The SDCCAG8 c.481C>T variant is predicted to result in premature protein termination (p.Gln161*). This variant has been reported in the homozygous state in an individual with autosomal recessive retinitis pigmentosa and kidney failure (Biswas et al. 2021. PubMed ID: 34662339). This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD. In ClinVar, this variant is interpreted as pathogenic (https://preview.ncbi.nlm.nih.gov/clinvar/variation/212140/). Nonsense variants in SDCCAG8 are expected to be pathogenic (Otto et al. 2010. PubMed ID: 20835237). This variant is interpreted as pathogenic. - |
Senior-Loken syndrome 7 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 09, 2015 | - - |
Senior-Loken syndrome 7;C3889474:Bardet-Biedl syndrome 16 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | May 24, 2023 | This sequence change creates a premature translational stop signal (p.Gln161*) in the SDCCAG8 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SDCCAG8 are known to be pathogenic (PMID: 20835237, 22190896). This variant is present in population databases (rs797045947, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with SDCCAG8-related conditions. ClinVar contains an entry for this variant (Variation ID: 212140). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A;A
Vest4
GERP RS
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