NM_000080.4(CHRNE):c.971del (p.Ile324fs) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 20, 2023
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:: RCV000326857.13

Allele description [Variation Report for NM_000080.4(CHRNE):c.971del (p.Ile324fs)]

NM_000080.4(CHRNE):c.971del (p.Ile324fs)

Gene:

CHRNE:cholinergic receptor nicotinic epsilon subunit [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_000080.4(CHRNE):c.971del (p.Ile324fs)

HGVS:

NC_000017.11:g.4899529del
NG_008029.2:g.8547del
NG_028005.1:g.71190del
NM_000080.4:c.971delMANE SELECT
NP_000071.1:p.Ile324fs
LRG_1254t1:c.971del
LRG_1254:g.8547del
LRG_1254p1:p.Ile324fs
NC_000017.10:g.4802824del
NM_000080.3:c.971del
NM_000080.3:c.971delT
NM_000080.4:c.971delTMANE SELECT

Protein change:

I324fs

Links:

OMIM: 100725.0006; dbSNP: rs879255562

NCBI 1000 Genomes Browser:

rs879255562

Molecular consequence:

NM_000080.4:c.971del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329296	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jul 20, 2023)	germline	clinical testing	Citation Link,
SCV000340606	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Apr 5, 2016)	germline	clinical testing	Citation Link,
SCV002019305	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 24, 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

SCV000329296

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jul 20, 2023)

germline

clinical testing

Citation Link,

SCV000340606

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Apr 5, 2016)

germline

clinical testing

Citation Link,

SCV002019305

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 24, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

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 GeneDx, SCV000329296.8

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

Description

Using alternate nomenclature (c.911delT), reported in association with autosomal recessive congenital myasthenia syndrome when in trans with another disease-causing variant (Sieb et al., 2000; Burke et al., 2004; Muller et al., 2005); Expression of variant in HEK 293 cells showed decreased cell surface expression of the protein (Burke et al., 2004); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 11030414, 15145336, 16087917, 9443457, 29395675)

#	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 Eurofins Ntd Llc (ga), SCV000340606.4

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

#	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		1	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002019305.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	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: Sep 29, 2024

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