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NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu) AND Familial focal epilepsy with variable foci

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 28, 2024
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:
RCV001034651.14

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:
Familial focal epilepsy with variable foci (FPEVF)
Identifiers:
MONDO: MONDO:0020310; MedGen: C1858477; OMIM: PS604364

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000546537Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 28, 2024) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Proline-rich transmembrane protein 2-negative paroxysmal kinesigenic dyskinesia: Clinical and genetic analyses of 163 patients.

Tian WT, Huang XJ, Mao X, Liu Q, Liu XL, Zeng S, Guo XN, Shen JY, Xu YQ, Tang HD, Yin XM, Zhang M, Tang WG, Liu XR, Tang BS, Chen SD, Cao L.

Mov Disord. 2018 Mar;33(3):459-467. doi: 10.1002/mds.27274. Epub 2018 Jan 22.

PubMed [citation]
PMID:
29356177
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000546537.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 1104 of the DEPDC5 protein (p.Ser1104Leu). This variant is present in population databases (rs79027628, gnomAD 0.03%). This missense change has been observed in individual(s) with clinical features of DEPDC5-related conditions (PMID: 23542697, 29356177, 31139143, 31594065). ClinVar contains an entry for this variant (Variation ID: 210846). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024