NM_001077350.3(NPRL3):c.1544+3_1544+5del AND Epilepsy, familial focal, with variable foci 3

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 2, 2020
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:: RCV001070835.5

Allele description [Variation Report for NM_001077350.3(NPRL3):c.1544+3_1544+5del]

NM_001077350.3(NPRL3):c.1544+3_1544+5del

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:

NM_001077350.3(NPRL3):c.1544+3_1544+5del

HGVS:

NC_000016.10:g.88693_88695del
NG_029669.1:g.55005_55007del
NG_042799.1:g.986_988del
NM_001039476.3:c.1007+3_1007+5del
NM_001077350.3:c.1544+3_1544+5delMANE SELECT
NM_001243247.2:c.1310+3_1310+5del
NM_001243248.2:c.1469+3_1469+5del
NM_001243249.2:c.1469+3_1469+5del
NC_000016.9:g.138692_138694del
NM_001077350.2:c.1544+3_1544+5del

Links:

dbSNP: rs1898611086

NCBI 1000 Genomes Browser:

rs1898611086

Molecular consequence:

NM_001039476.3:c.1007+3_1007+5del - intron variant - [Sequence Ontology: SO:0001627]
NM_001077350.3:c.1544+3_1544+5del - intron variant - [Sequence Ontology: SO:0001627]
NM_001243247.2:c.1310+3_1310+5del - intron variant - [Sequence Ontology: SO:0001627]
NM_001243248.2:c.1469+3_1469+5del - intron variant - [Sequence Ontology: SO:0001627]
NM_001243249.2:c.1469+3_1469+5del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001236109	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 2, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001236109

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 2, 2020)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001236109.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

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. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). This variant has not been reported in the literature in individuals with NPRL3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 13 of the NPRL3 gene. It does not directly change the encoded amino acid sequence of the NPRL3 protein, but it affects a nucleotide within the consensus splice site of the intron.

#	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 20, 2024

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