NM_001077350.3(NPRL3):c.1559dup (p.Arg521fs) AND Epilepsy, familial focal, with variable foci 3

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 30, 2024
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:: RCV001775430.5

Allele description [Variation Report for NM_001077350.3(NPRL3):c.1559dup (p.Arg521fs)]

NM_001077350.3(NPRL3):c.1559dup (p.Arg521fs)

Gene:

NPRL3:NPR3 like, GATOR1 complex subunit [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_001077350.3(NPRL3):c.1559dup (p.Arg521fs)

HGVS:

NC_000016.10:g.86857dup
NG_029669.1:g.56844dup
NM_001039476.2:c.1022dup
NM_001039476.3:c.1022dup
NM_001077350.3:c.1559dupMANE SELECT
NM_001243247.2:c.1325dup
NM_001243248.2:c.1484dup
NM_001243249.2:c.1484dup
NP_001034565.1:p.Arg342fs
NP_001070818.1:p.Arg521fs
NP_001230176.1:p.Arg443fs
NP_001230177.1:p.Arg496fs
NP_001230178.1:p.Arg496fs
NC_000016.9:g.136856dup
NM_001077350.3:c.1559dup
NM_001243249.1:c.1483dup

Protein change:

R342fs

Links:

dbSNP: rs2141895084

NCBI 1000 Genomes Browser:

rs2141895084

Molecular consequence:

NM_001039476.3:c.1022dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001077350.3:c.1559dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243247.2:c.1325dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243248.2:c.1484dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243249.2:c.1484dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Epilepsy, familial focal, with variable foci 3 (FFEVF3)
Identifiers:: MONDO: MONDO:0014925; MedGen: C4310708; OMIM: 617118

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002012316	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 30, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004805331	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 25, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002012316

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 30, 2024)

germline

clinical testing

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

SCV004805331

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 25, 2024)

germline

research

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

Citations

PubMed

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 3billion, SCV002012316.2

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

Description

The variant is not observed in the gnomAD v4.0.0 dataset. Frameshift (nonsense) - predicted to result in a loss or disruption of normal protein function through protein truncation. Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

#	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 Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004805331.2

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

#	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: Aug 11, 2024

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