NC_000016.10:g.(?_130502)_(138287_?)del AND Epilepsy, familial focal, with variable foci 3

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 2, 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:: RCV000653316.3

Allele description [Variation Report for NC_000016.10:g.(?_130502)_(138287_?)del]

NC_000016.10:g.(?_130502)_(138287_?)del

Genes:

NPRL3:NPR3 like, GATOR1 complex subunit [Gene - OMIM - HGNC]
HBA-LCR:alpha-globin locus control region [Gene]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NC_000016.10:g.(?_130502)_(138287_?)del

HGVS:

NC_000016.10:g.(?_130502)_(138287_?)del
NC_000016.9:g.(?_180501)_(188286_?)del

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
SCV000775195	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 2, 2019)	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

SCV000775195

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 2, 2019)

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, SCV000775195.3

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

Description

This variant is a gross deletion of the genomic region encompassing exons 2-3 of the NPRL3 gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 3 of the NPRL3 gene. This is expected to result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with NPRL3-related disease. Loss-of-function variants in NPRL3 are known to be pathogenic (PMID: 26285051, 26505888). For these reasons, this variant has been classified as Pathogenic.

#	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 23, 2022

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