NM_001242896.3(DEPDC5):c.1355C>T (p.Ala452Val) AND Inborn genetic diseases

Germline classification:: Benign (1 submission)
Last evaluated:: Oct 25, 2016
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002313991.9

Allele description [Variation Report for NM_001242896.3(DEPDC5):c.1355C>T (p.Ala452Val)]

NM_001242896.3(DEPDC5):c.1355C>T (p.Ala452Val)

Gene:

DEPDC5:DEP domain containing 5, GATOR1 subcomplex subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_001242896.3(DEPDC5):c.1355C>T (p.Ala452Val)

HGVS:

NC_000022.11:g.31810551C>T
NG_034067.1:g.61601C>T
NM_001007188.4:c.1355C>T
NM_001136029.4:c.1355C>T
NM_001242896.3:c.1355C>TMANE SELECT
NM_001242897.2:c.1355C>T
NM_001363852.2:c.1355C>T
NM_001363854.2:c.1355C>T
NM_001364318.2:c.1355C>T
NM_001364319.2:c.1355C>T
NM_001364320.2:c.1355C>T
NM_001369901.1:c.1271C>T
NM_001369902.1:c.1271C>T
NM_001369903.1:c.1355C>T
NM_014662.6:c.1355C>T
NP_001007189.1:p.Ala452Val
NP_001129501.1:p.Ala452Val
NP_001229825.1:p.Ala452Val
NP_001229826.1:p.Ala452Val
NP_001350781.1:p.Ala452Val
NP_001350783.1:p.Ala452Val
NP_001351247.1:p.Ala452Val
NP_001351248.1:p.Ala452Val
NP_001351249.1:p.Ala452Val
NP_001356830.1:p.Ala424Val
NP_001356831.1:p.Ala424Val
NP_001356832.1:p.Ala452Val
NP_055477.1:p.Ala452Val
NC_000022.10:g.32206537C>T
NM_001242896.1:c.1355C>T
NR_110988.2:n.1561C>T
NR_146296.2:n.1444C>T
NR_157125.2:n.1440C>T
NR_157126.2:n.1444C>T
NR_157128.1:n.1561C>T
O75140:p.Ala452Val

Protein change:

A424V

Links:

UniProtKB: O75140#VAR_069263; dbSNP: rs202226316

NCBI 1000 Genomes Browser:

rs202226316

Molecular consequence:

NM_001007188.4:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136029.4:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242896.3:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242897.2:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363852.2:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363854.2:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364318.2:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364319.2:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364320.2:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369901.1:c.1271C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369902.1:c.1271C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369903.1:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014662.6:c.1355C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_110988.2:n.1561C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146296.2:n.1444C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157125.2:n.1440C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157126.2:n.1444C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157128.1:n.1561C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000848141	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Oct 25, 2016)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23542697, 25366275 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000848141

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Oct 25, 2016)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in DEPDC5 cause familial focal epilepsy with variable foci.

Dibbens LM, de Vries B, Donatello S, Heron SE, Hodgson BL, Chintawar S, Crompton DE, Hughes JN, Bellows ST, Klein KM, Callenbach PM, Corbett MA, Gardner AE, Kivity S, Iona X, Regan BM, Weller CM, Crimmins D, O'Brien TJ, Guerrero-López R, Mulley JC, Dubeau F, et al.

Nat Genet. 2013 May;45(5):546-51. doi: 10.1038/ng.2599. Epub 2013 Mar 31.

PubMed [citation]

PMID:: 23542697

Preliminary functional assessment and classification of DEPDC5 variants associated with focal epilepsy.

van Kranenburg M, Hoogeveen-Westerveld M, Nellist M.

Hum Mutat. 2015 Feb;36(2):200-9. doi: 10.1002/humu.22723. Epub 2014 Nov 27.

PubMed [citation]

PMID:: 25366275

Details of each submission

From Ambry Genetics, SCV000848141.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 9, 2024

ClinVar

Relating variation to medicine