NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu) AND Inborn genetic diseases

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 19, 2019
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:: RCV002317677.9

Allele description [Variation Report for NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu)]

NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu)

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.3311C>T (p.Ser1104Leu)

HGVS:

NC_000022.11:g.31861414C>T
NG_034067.1:g.112464C>T
NM_001136029.4:c.3284C>T
NM_001242896.3:c.3311C>TMANE SELECT
NM_001242897.2:c.3030+3861C>T
NM_001363852.2:c.3264+3861C>T
NM_001363854.2:c.3077C>T
NM_001364318.2:c.3311C>T
NM_001364319.2:c.3077C>T
NM_001364320.2:c.3264+3861C>T
NM_001369901.1:c.3227C>T
NM_001369902.1:c.3227C>T
NM_001369903.1:c.3237+3861C>T
NM_014662.6:c.3237+3861C>T
NP_001129501.1:p.Ser1095Leu
NP_001229825.1:p.Ser1104Leu
NP_001229825.1:p.Ser1104Leu
NP_001350783.1:p.Ser1026Leu
NP_001351247.1:p.Ser1104Leu
NP_001351248.1:p.Ser1026Leu
NP_001356830.1:p.Ser1076Leu
NP_001356831.1:p.Ser1076Leu
NC_000022.10:g.32257400C>T
NM_001242896.1:c.3311C>T
NR_146296.2:n.3400C>T
NR_157126.2:n.3400C>T
O75140:p.Ser1104Leu

Protein change:

S1026L

Links:

UniProtKB: O75140#VAR_069266; dbSNP: rs79027628

NCBI 1000 Genomes Browser:

rs79027628

Molecular consequence:

NM_001242897.2:c.3030+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001363852.2:c.3264+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001364320.2:c.3264+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001369903.1:c.3237+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_014662.6:c.3237+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001136029.4:c.3284C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242896.3:c.3311C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363854.2:c.3077C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364318.2:c.3311C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364319.2:c.3077C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369901.1:c.3227C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369902.1:c.3227C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_146296.2:n.3400C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157126.2:n.3400C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000851156	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jun 19, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20864493, 23542697 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000851156

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jun 19, 2019)

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

Familial mesial temporal lobe epilepsy: a benign epilepsy syndrome showing complex inheritance.

Crompton DE, Scheffer IE, Taylor I, Cook MJ, McKelvie PA, Vears DF, Lawrence KM, McMahon JM, Grinton BE, McIntosh AM, Berkovic SF.

Brain. 2010 Nov;133(11):3221-31. doi: 10.1093/brain/awq251. Epub 2010 Sep 23.

PubMed [citation]

PMID:: 20864493

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

Details of each submission

From Ambry Genetics, SCV000851156.4

#	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 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.

#	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: Nov 10, 2024

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