NM_000744.7(CHRNA4):c.956T>A (p.Leu319Gln) 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:: Oct 12, 2022
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:: RCV003065819.2

Allele description

NM_000744.7(CHRNA4):c.956T>A (p.Leu319Gln)

Gene:

CHRNA4:cholinergic receptor nicotinic alpha 4 subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.33

Genomic location:

Preferred name:

NM_000744.7(CHRNA4):c.956T>A (p.Leu319Gln)

HGVS:

NC_000020.11:g.63350455A>T
NG_011931.1:g.15889T>A
NM_000744.7:c.956T>AMANE SELECT
NM_001256573.2:c.428T>A
NP_000735.1:p.Leu319Gln
NP_001243502.1:p.Leu143Gln
NC_000020.10:g.61981807A>T
NR_046317.2:n.1165T>A

Protein change:

L143Q

Molecular consequence:

NM_000744.7:c.956T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001256573.2:c.428T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046317.2:n.1165T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

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AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase, partial [Lelliottia sp....
AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase, partial [Lelliottia sp. RWM.1]
gi|1983701695|ref|WP_203452781.1|

Protein
MRPS5P3 mitochondrial ribosomal protein S5 pseudogene 3 [Homo sapiens]
MRPS5P3 mitochondrial ribosomal protein S5 pseudogene 3 [Homo sapiens]
Gene ID:133615

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003351051	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 12, 2022)	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

SCV003351051

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 12, 2022)

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

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003351051.2

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CHRNA4 protein function. 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. This variant has not been reported in the literature in individuals affected with CHRNA4-related conditions. This sequence change replaces leucine, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 319 of the CHRNA4 protein (p.Leu319Gln). This variant is present in population databases (no rsID available, gnomAD 0.006%).

#	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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