NM_001242896.3(DEPDC5):c.1475G>A (p.Arg492Gln) AND Familial focal epilepsy with variable foci

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 24, 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:: RCV001066813.7

Allele description [Variation Report for NM_001242896.3(DEPDC5):c.1475G>A (p.Arg492Gln)]

NM_001242896.3(DEPDC5):c.1475G>A (p.Arg492Gln)

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.1475G>A (p.Arg492Gln)

HGVS:

NC_000022.11:g.31815021G>A
NG_034067.1:g.66071G>A
NM_001007188.4:c.1475G>A
NM_001136029.4:c.1475G>A
NM_001242896.3:c.1475G>AMANE SELECT
NM_001242897.2:c.1475G>A
NM_001363852.2:c.1475G>A
NM_001363854.2:c.1475G>A
NM_001364318.2:c.1475G>A
NM_001364319.2:c.1475G>A
NM_001364320.2:c.1475G>A
NM_001369901.1:c.1391G>A
NM_001369902.1:c.1391G>A
NM_001369903.1:c.1475G>A
NM_014662.6:c.1475G>A
NP_001007189.1:p.Arg492Gln
NP_001129501.1:p.Arg492Gln
NP_001229825.1:p.Arg492Gln
NP_001229826.1:p.Arg492Gln
NP_001350781.1:p.Arg492Gln
NP_001350783.1:p.Arg492Gln
NP_001351247.1:p.Arg492Gln
NP_001351248.1:p.Arg492Gln
NP_001351249.1:p.Arg492Gln
NP_001356830.1:p.Arg464Gln
NP_001356831.1:p.Arg464Gln
NP_001356832.1:p.Arg492Gln
NP_055477.1:p.Arg492Gln
NC_000022.10:g.32211007G>A
NM_001242896.1:c.1475G>A
NR_110988.2:n.1681G>A
NR_146296.2:n.1564G>A
NR_157125.2:n.1560G>A
NR_157126.2:n.1564G>A
NR_157128.1:n.1681G>A

Protein change:

R464Q

Links:

dbSNP: rs745893053

NCBI 1000 Genomes Browser:

rs745893053

Molecular consequence:

NM_001007188.4:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001136029.4:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001242896.3:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001242897.2:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363852.2:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363854.2:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364318.2:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364319.2:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364320.2:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369901.1:c.1391G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369902.1:c.1391G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369903.1:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014662.6:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_110988.2:n.1681G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146296.2:n.1564G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157125.2:n.1560G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157126.2:n.1564G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157128.1:n.1681G>A - 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
SCV001231833	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 24, 2024)	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

SCV001231833

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 24, 2024)

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, SCV001231833.5

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 492 of the DEPDC5 protein (p.Arg492Gln). This variant is present in population databases (rs745893053, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with DEPDC5-related conditions. ClinVar contains an entry for this variant (Variation ID: 860499). 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.

#	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: Feb 28, 2024

ClinVar

Relating variation to medicine