NC_000020.10:g.(?_61977556)_(62562941_?)dup AND Autosomal dominant nocturnal frontal lobe epilepsy

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 4, 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:: RCV001033704.1

Allele description

NC_000020.10:g.(?_61977556)_(62562941_?)dup

Genes:

ARFRP1:ADP ribosylation factor related protein 1 [Gene - OMIM - HGNC]
DNAJC5:DnaJ heat shock protein family (Hsp40) member C5 [Gene - OMIM - HGNC]
LIME1:Lck interacting transmembrane adaptor 1 [Gene - OMIM - HGNC]
SLC2A4RG:SLC2A4 regulator [Gene - OMIM - HGNC]
TNFRSF6B:TNF receptor superfamily member 6b [Gene - OMIM - HGNC]
TPD52L2:TPD52 like 2 [Gene - OMIM - HGNC]
ABHD16B:abhydrolase domain containing 16B [Gene - HGNC]
CHRNA4:cholinergic receptor nicotinic alpha 4 subunit [Gene - OMIM - HGNC]
EEF1A2:eukaryotic translation elongation factor 1 alpha 2 [Gene - OMIM - HGNC]
FNDC11:fibronectin type III domain containing 11 [Gene - HGNC]
GMEB2:glucocorticoid modulatory element binding protein 2 [Gene - OMIM - HGNC]
HELZ2:helicase with zinc finger 2 [Gene - OMIM - HGNC]
PPDPF:pancreatic progenitor cell differentiation and proliferation factor [Gene - HGNC]
KCNQ2:potassium voltage-gated channel subfamily Q member 2 [Gene - OMIM - HGNC]
PTK6:protein tyrosine kinase 6 [Gene - OMIM - HGNC]
RTEL1:regulator of telomere elongation helicase 1 [Gene - OMIM - HGNC]
SRMS:src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites [Gene - OMIM - HGNC]
STMN3:stathmin 3 [Gene - OMIM - HGNC]
ZGPAT:zinc finger CCCH-type and G-patch domain containing [Gene - OMIM - HGNC]
ZBTB46:zinc finger and BTB domain containing 46 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

20q13.33

Genomic location:

Chr20: 61977556 - 62562941 (on Assembly GRCh37)

Preferred name:

NC_000020.10:g.(?_61977556)_(62562941_?)dup

HGVS:

NC_000020.10:g.(?_61977556)_(62562941_?)dup

Condition(s)

Name:: Autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE)
Identifiers:: MONDO: MONDO:0020300; MedGen: C3696898

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001197011	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 4, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25921748, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001197011

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 4, 2019)

germline

clinical testing

PubMed (2)
[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

Array-comparative genomic hybridization analysis of a cohort of Saudi patients with epilepsy.

Faheem M, Naseer MI, Chaudhary AG, Kumosani TA, Rasool M, Algahtani HA, Bibi F, Kamal MA, Al-Qahtani MH.

CNS Neurol Disord Drug Targets. 2015;14(4):468-75.

PubMed [citation]

PMID:: 25921748

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001197011.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the CHRNA4 gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. Isolated whole-gene copy number gains of CHRNA4 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 25921748). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. 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.

#	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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