rs185576553
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2
The NM_001242896.3(DEPDC5):āc.2672G>Cā(p.Ser891Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00057 in 1,613,524 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.00022 ( 0 hom., cov: 32)
Exomes š: 0.00061 ( 2 hom. )
Consequence
DEPDC5
NM_001242896.3 missense
NM_001242896.3 missense
Scores
1
7
11
Clinical Significance
Conservation
PhyloP100: 7.09
Genes affected
DEPDC5 (HGNC:18423): (DEP domain containing 5, GATOR1 subcomplex subunit) This gene encodes a member of the IML1 family of proteins involved in G-protein signaling pathways. The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cell growth by sensing the availability of nutrients. The protein encoded by this gene is a component of the GATOR1 (GAP activity toward Rags) complex which inhibits the amino acid-sensing branch of the mTORC1 pathway. Mutations in this gene are associated with autosomal dominant familial focal epilepsy with variable foci. A single nucleotide polymorphism in an intron of this gene has been associated with an increased risk of hepatocellular carcinoma in individuals with chronic hepatitis C virus infection. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), DEPDC5. . Gene score misZ 2.6501 (greater than the threshold 3.09). Trascript score misZ 3.7275 (greater than threshold 3.09). GenCC has associacion of gene with focal epilepsy, Brugada syndrome, epilepsy, familial focal, with variable foci 1, familial focal epilepsy with variable foci, autosomal dominant epilepsy with auditory features, autosomal dominant nocturnal frontal lobe epilepsy.
BP4
Computational evidence support a benign effect (MetaRNN=0.06469008).
BP6
Variant 22-31843683-G-C is Benign according to our data. Variant chr22-31843683-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 407353.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=4, Uncertain_significance=2}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000223 (34/152310) while in subpopulation NFE AF= 0.00047 (32/68032). AF 95% confidence interval is 0.000342. There are 0 homozygotes in gnomad4. There are 18 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DEPDC5 | NM_001242896.3 | c.2672G>C | p.Ser891Thr | missense_variant | 29/43 | ENST00000651528.2 | NP_001229825.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.2672G>C | p.Ser891Thr | missense_variant | 29/43 | NM_001242896.3 | ENSP00000498382.1 | |||
ENSG00000285404 | ENST00000646701.1 | c.1786+24458G>C | intron_variant | ENSP00000496158.1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000228 AC: 57AN: 249536Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135378
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GnomAD4 exome AF: 0.000606 AC: 885AN: 1461214Hom.: 2 Cov.: 31 AF XY: 0.000614 AC XY: 446AN XY: 726798
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GnomAD4 genome AF: 0.000223 AC: 34AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74480
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:4
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2020 | - - |
Familial focal epilepsy with variable foci Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 27, 2024 | This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 891 of the DEPDC5 protein (p.Ser891Thr). This variant is present in population databases (rs185576553, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with DEPDC5-related conditions. ClinVar contains an entry for this variant (Variation ID: 407353). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
DEPDC5-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 29, 2024 | The DEPDC5 c.2672G>C variant is predicted to result in the amino acid substitution p.Ser891Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.048% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 17, 2024 | Variant summary: DEPDC5 c.2672G>C (p.Ser891Thr) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00057 in 1613524 control chromosomes in the gnomAD database (v4.0.0), including 2 homozygotes, suggesting a benign role for the variant. To our knowledge, no occurrence of c.2672G>C in individuals affected with Epilepsy, Familial Focal, With Variable Foci 1 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 407353). Based on the evidence outlined above, the variant was classified as likely benign. - |
Epilepsy, familial focal, with variable foci 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 09, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 28, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;.;.;.;T;.;.;.;.;T;.;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;.;.;D;D;.;D;.;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;M;.;.;M;.;.;.;.;M;.;M;M;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.;.;.;.;N;.;.;.;N;.;.;N;.
REVEL
Benign
Sift
Uncertain
D;.;.;.;.;.;D;.;.;.;T;.;.;T;.
Sift4G
Benign
T;.;.;.;.;.;D;.;.;.;D;.;.;T;.
Polyphen
0.87
.;.;P;.;.;.;.;.;.;.;.;.;P;.;.
Vest4
MVP
MPC
0.41
ClinPred
T
GERP RS
Varity_R
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