NM_001242896.3(DEPDC5):c.3461C>T (p.Ser1154Phe) AND not provided

Germline classification:: Uncertain significance (4 submissions)
Last evaluated:: Feb 1, 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:: RCV000991883.13

Allele description [Variation Report for NM_001242896.3(DEPDC5):c.3461C>T (p.Ser1154Phe)]

NM_001242896.3(DEPDC5):c.3461C>T (p.Ser1154Phe)

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.3461C>T (p.Ser1154Phe)

HGVS:

NC_000022.11:g.31870720C>T
NG_034067.1:g.121770C>T
NM_001136029.4:c.3434C>T
NM_001242896.3:c.3461C>TMANE SELECT
NM_001242897.2:c.3161C>T
NM_001363852.2:c.3395C>T
NM_001363854.2:c.3227C>T
NM_001364318.2:c.3461C>T
NM_001364319.2:c.3227C>T
NM_001364320.2:c.3395C>T
NM_001369901.1:c.3377C>T
NM_001369902.1:c.3377C>T
NM_001369903.1:c.3368C>T
NM_014662.6:c.3368C>T
NP_001129501.1:p.Ser1145Phe
NP_001229825.1:p.Ser1154Phe
NP_001229826.1:p.Ser1054Phe
NP_001350781.1:p.Ser1132Phe
NP_001350783.1:p.Ser1076Phe
NP_001351247.1:p.Ser1154Phe
NP_001351248.1:p.Ser1076Phe
NP_001351249.1:p.Ser1132Phe
NP_001356830.1:p.Ser1126Phe
NP_001356831.1:p.Ser1126Phe
NP_001356832.1:p.Ser1123Phe
NP_055477.1:p.Ser1123Phe
NC_000022.10:g.32266706C>T
NM_001242896.1:c.3461C>T
NR_110988.2:n.3367C>T
NR_146296.2:n.3550C>T
NR_157125.2:n.3358C>T
NR_157126.2:n.3550C>T
NR_157128.1:n.3601C>T
O75140:p.Ser1154Phe

Protein change:

S1054F

Links:

UniProtKB: O75140#VAR_077132; dbSNP: rs578244490

NCBI 1000 Genomes Browser:

rs578244490

Molecular consequence:

NM_001136029.4:c.3434C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242896.3:c.3461C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242897.2:c.3161C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363852.2:c.3395C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363854.2:c.3227C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364318.2:c.3461C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364319.2:c.3227C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364320.2:c.3395C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369901.1:c.3377C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369902.1:c.3377C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369903.1:c.3368C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014662.6:c.3368C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_110988.2:n.3367C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146296.2:n.3550C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157125.2:n.3358C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157126.2:n.3550C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157128.1:n.3601C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001143718	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Feb 1, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26505888, 26467025
SCV001743102	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV001932839	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV002037803	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing

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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in the mammalian target of rapamycin pathway regulators NPRL2 and NPRL3 cause focal epilepsy.

Ricos MG, Hodgson BL, Pippucci T, Saidin A, Ong YS, Heron SE, Licchetta L, Bisulli F, Bayly MA, Hughes J, Baldassari S, Palombo F; Epilepsy Electroclinical Study Group., Santucci M, Meletti S, Berkovic SF, Rubboli G, Thomas PQ, Scheffer IE, Tinuper P, Geoghegan J, Schreiber AW, et al.

Ann Neurol. 2016 Jan;79(1):120-31. doi: 10.1002/ana.24547. Epub 2015 Dec 12.

PubMed [citation]

PMID:: 26505888

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Athena Diagnostics Inc, SCV001143718.1

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

#	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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001743102.3

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

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001932839.1

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

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV002037803.1

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

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

Last Updated: Apr 20, 2024

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