NM_003647.3(DGKE):c.966G>A (p.Trp322Ter) AND Immunoglobulin-mediated membranoproliferative glomerulonephritis

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Apr 7, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000760165.9

Allele description [Variation Report for NM_003647.3(DGKE):c.966G>A (p.Trp322Ter)]

NM_003647.3(DGKE):c.966G>A (p.Trp322Ter)

Gene:

DGKE:diacylglycerol kinase epsilon [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q22

Genomic location:

Preferred name:

NM_003647.3(DGKE):c.966G>A (p.Trp322Ter)

HGVS:

NC_000017.11:g.56848773G>A
NG_033888.1:g.19675G>A
NM_003647.3:c.966G>AMANE SELECT
NP_003638.1:p.Trp322Ter
NC_000017.10:g.54926134G>A
NM_003647.2:c.966G>A
p.Trp322*
p.Trp322X

Protein change:

W322*; TRP322TER

Links:

OMIM: 601440.0004; dbSNP: rs138924661

NCBI 1000 Genomes Browser:

rs138924661

Molecular consequence:

NM_003647.3:c.966G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Immunoglobulin-mediated membranoproliferative glomerulonephritis
Synonyms:: NEPHROTIC SYNDROME, TYPE 7, WITH MEMBRANOPROLIFERATIVE GLOMERULONEPHRITIS; Nephrotic syndrome, type 7
Identifiers:: MONDO: MONDO:0014005; MedGen: C3554330; OMIM: 615008

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000889982	Center for Precision Medicine, Vanderbilt University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 16, 2018)	germline	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 29590070
SCV001368100	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 12, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002810357	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 7, 2022)	unknown	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

SCV000889982

Center for Precision Medicine, Vanderbilt University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 16, 2018)

germline

research

PubMed (2)
[See all records that cite these PMIDs]

SCV001368100

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 12, 2019)

unknown

clinical testing

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

SCV002810357

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 7, 2022)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	15	not provided	not provided	not provided	not provided	research
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns.

Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Van Driest SL, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, Ruderfer D, Velez Edwards DR, Hamid R, Cogan J, Glazer A, Wei WQ, Feng Q, et al.

Science. 2018 Mar 16;359(6381):1233-1239. doi: 10.1126/science.aal4043.

PubMed [citation]

PMID:: 29590070
PMCID:: PMC5959723

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Precision Medicine, Vanderbilt University Medical Center, SCV000889982.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	15	not provided	not provided	research	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	discovery		15	not provided	not provided	not provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001368100.2

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

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2.

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

From Fulgent Genetics, Fulgent Genetics, SCV002810357.1

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

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

Last Updated: Apr 7, 2025

ClinVar

Relating variation to medicine