ClinVar Genomic variation as it relates to human health
NM_001242896.3(DEPDC5):c.2020C>T (p.Arg674Cys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001242896.3(DEPDC5):c.2020C>T (p.Arg674Cys)
Variation ID: 238673 Accession: VCV000238673.32
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 22q12.3 22: 31822706 (GRCh38) [ NCBI UCSC ] 22: 32218692 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 5, 2017 May 1, 2024 Jan 17, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001242896.3:c.2020C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001229825.1:p.Arg674Cys missense NM_001136029.4:c.2020C>T NP_001129501.1:p.Arg674Cys missense NM_001242897.2:c.1870+3481C>T intron variant NM_001363852.2:c.2020C>T NP_001350781.1:p.Arg674Cys missense NM_001363854.2:c.1870+3481C>T intron variant NM_001364318.2:c.2020C>T NP_001351247.1:p.Arg674Cys missense NM_001364319.2:c.1870+3481C>T intron variant NM_001364320.2:c.2020C>T NP_001351249.1:p.Arg674Cys missense NM_001369901.1:c.1936C>T NP_001356830.1:p.Arg646Cys missense NM_001369902.1:c.1936C>T NP_001356831.1:p.Arg646Cys missense NM_001369903.1:c.2020C>T NP_001356832.1:p.Arg674Cys missense NM_014662.6:c.2020C>T NP_055477.1:p.Arg674Cys missense NR_146296.2:n.2109C>T non-coding transcript variant NR_157125.2:n.2105C>T non-coding transcript variant NR_157126.2:n.2109C>T non-coding transcript variant NR_157128.1:n.2226C>T non-coding transcript variant NC_000022.11:g.31822706C>T NC_000022.10:g.32218692C>T NG_034067.1:g.73756C>T - Protein change
- R674C, R646C
- Other names
- -
- Canonical SPDI
- NC_000022.11:31822705:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00100 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.00094
1000 Genomes Project 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00167
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00196
The Genome Aggregation Database (gnomAD) 0.00218
The Genome Aggregation Database (gnomAD), exomes 0.00218
Exome Aggregation Consortium (ExAC) 0.00246
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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DEPDC5 | - | - |
GRCh38 GRCh37 |
2270 | 2298 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Benign/Likely benign (5) |
criteria provided, multiple submitters, no conflicts
|
Jul 1, 2023 | RCV000513993.23 | |
Pathogenic (1) |
no assertion criteria provided
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Jan 1, 2017 | RCV000656069.9 | |
Benign/Likely benign (3) |
criteria provided, multiple submitters, no conflicts
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Nov 7, 2021 | RCV000990423.11 | |
Benign (1) |
criteria provided, single submitter
|
Jan 17, 2024 | RCV001080161.12 | |
Benign (1) |
criteria provided, single submitter
|
Oct 24, 2016 | RCV002315690.9 | |
Likely benign (1) |
criteria provided, single submitter
|
Feb 5, 2020 | RCV003919942.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely benign
(Jun 29, 2017)
|
criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
|
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000610347.1
First in ClinVar: Nov 05, 2017 Last updated: Nov 05, 2017 |
|
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Likely benign
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Epilepsy, familial focal, with variable foci 1
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001141408.1
First in ClinVar: Jan 12, 2020 Last updated: Jan 12, 2020 |
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Likely benign
(Jan 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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Epilepsy, familial focal, with variable foci 1
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001440757.1
First in ClinVar: Oct 30, 2020 Last updated: Oct 30, 2020 |
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Benign
(Nov 07, 2021)
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criteria provided, single submitter
Method: clinical testing
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Epilepsy, familial focal, with variable foci 1
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV002039967.1
First in ClinVar: Dec 25, 2021 Last updated: Dec 25, 2021 |
|
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Benign
(Sep 26, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001945854.2
First in ClinVar: Sep 29, 2021 Last updated: Mar 04, 2023 |
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Benign
(Jan 17, 2024)
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criteria provided, single submitter
Method: clinical testing
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Familial focal epilepsy with variable foci
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000286364.10
First in ClinVar: Jul 01, 2016 Last updated: Feb 28, 2024 |
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Likely benign
(Feb 05, 2020)
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criteria provided, single submitter
Method: clinical testing
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DEPDC5-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004728985.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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Likely benign
(Jul 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV002563717.10
First in ClinVar: Aug 23, 2022 Last updated: Apr 15, 2024 |
Comment:
DEPDC5: BP4, BS1
Number of individuals with the variant: 6
|
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Benign
(Oct 24, 2016)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000848854.4
First in ClinVar: Nov 08, 2018 Last updated: May 01, 2024 |
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more)
This alteration is classified as 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. (less)
|
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Pathogenic
(Jan 01, 2017)
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no assertion criteria provided
Method: case-control
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Childhood epilepsy with centrotemporal spikes
Affected status: yes
Allele origin:
germline
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Bioinformatics Core, Luxembourg Center for Systems Biomedicine
Study: EUROEPINOMICS COGIE
Accession: SCV000588345.1 First in ClinVar: Jun 01, 2018 Last updated: Jun 01, 2018 |
Comment:
CAADphred>15
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742215.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
|
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001928867.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy. | Bobbili DR | European journal of human genetics : EJHG | 2018 | PMID: 29358611 |
Text-mined citations for rs181347577 ...
HelpRecord last updated May 08, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.