NM_001242896.3(DEPDC5):c.373T>C (p.Cys125Arg) AND Familial focal epilepsy with variable foci

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 18, 2023
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:: RCV001204470.7

Allele description [Variation Report for NM_001242896.3(DEPDC5):c.373T>C (p.Cys125Arg)]

NM_001242896.3(DEPDC5):c.373T>C (p.Cys125Arg)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.2

Genomic location:

Preferred name:

NM_001242896.3(DEPDC5):c.373T>C (p.Cys125Arg)

HGVS:

NC_000022.11:g.31768823T>C
NG_034067.1:g.19873T>C
NM_001007188.4:c.373T>C
NM_001136029.4:c.373T>C
NM_001242896.3:c.373T>CMANE SELECT
NM_001242897.2:c.373T>C
NM_001363852.2:c.373T>C
NM_001363854.2:c.373T>C
NM_001364318.2:c.373T>C
NM_001364319.2:c.373T>C
NM_001364320.2:c.373T>C
NM_001369901.1:c.289T>C
NM_001369902.1:c.289T>C
NM_001369903.1:c.373T>C
NM_014662.6:c.373T>C
NP_001007189.1:p.Cys125Arg
NP_001129501.1:p.Cys125Arg
NP_001229825.1:p.Cys125Arg
NP_001229826.1:p.Cys125Arg
NP_001350781.1:p.Cys125Arg
NP_001350783.1:p.Cys125Arg
NP_001351247.1:p.Cys125Arg
NP_001351248.1:p.Cys125Arg
NP_001351249.1:p.Cys125Arg
NP_001356830.1:p.Cys97Arg
NP_001356831.1:p.Cys97Arg
NP_001356832.1:p.Cys125Arg
NP_055477.1:p.Cys125Arg
NC_000022.10:g.32164809T>C
NM_001242896.1:c.373T>C
NR_110988.2:n.579T>C
NR_146296.2:n.462T>C
NR_157125.2:n.462T>C
NR_157126.2:n.462T>C
NR_157128.1:n.579T>C
p.Cys125Arg

Protein change:

C125R

Links:

dbSNP: rs778986487

NCBI 1000 Genomes Browser:

rs778986487

Molecular consequence:

NM_001007188.4:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001136029.4:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242896.3:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242897.2:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363852.2:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363854.2:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001364318.2:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001364319.2:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001364320.2:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369901.1:c.289T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369902.1:c.289T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369903.1:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_014662.6:c.373T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_110988.2:n.579T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146296.2:n.462T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157125.2:n.462T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157126.2:n.462T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157128.1:n.579T>C - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001375677	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001375677

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 18, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001375677.5

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

Description

ClinVar contains an entry for this variant (Variation ID: 935803). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with DEPDC5-related conditions. This variant is present in population databases (rs778986487, gnomAD 0.002%). This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 125 of the DEPDC5 protein (p.Cys125Arg).

#	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: Apr 6, 2024

ClinVar

Relating variation to medicine