NM_005199.5(CHRNG):c.753_754del (p.Val253fs) AND not provided

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

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Jan 4, 2024
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:: RCV000282633.12

Allele description

NM_005199.5(CHRNG):c.753_754del (p.Val253fs)

Gene:

CHRNG:cholinergic receptor nicotinic gamma subunit [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q37.1

Genomic location:

Preferred name:

NM_005199.5(CHRNG):c.753_754del (p.Val253fs)

HGVS:

NC_000002.12:g.232543030_232543031del
NG_012954.2:g.8339_8340del
NM_005199.5:c.753_754delMANE SELECT
NP_005190.4:p.Val253Alafs
NP_005190.4:p.Val253fs
LRG_1275t1:c.753_754del
LRG_1275:g.8339_8340del
LRG_1275p1:p.Val253fs
NC_000002.11:g.233407740_233407741del
NC_000002.11:g.233407740_233407741del
NG_012954.1:g.8304_8305del
NM_005199.4:c.753_754del
NM_005199.4:c.753_754delCT
NM_005199.5:c.753_754delCTMANE SELECT

Protein change:

V253fs

Links:

OMIM: 100730.0007; dbSNP: rs767503038

NCBI 1000 Genomes Browser:

rs767503038

Molecular consequence:

NM_005199.5:c.753_754del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000329801	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 16, 2021)	germline	clinical testing	Citation Link,
SCV001905677	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002019314	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003195503	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 4, 2024)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 16826520, 16826531, 22167768, 24038971, 25608830, 27245440, 28492532

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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	1	not provided	clinical testing
not provided	germline	unknown	not provided	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

Escobar syndrome is a prenatal myasthenia caused by disruption of the acetylcholine receptor fetal gamma subunit.

Hoffmann K, Muller JS, Stricker S, Megarbane A, Rajab A, Lindner TH, Cohen M, Chouery E, Adaimy L, Ghanem I, Delague V, Boltshauser E, Talim B, Horvath R, Robinson PN, Lochmüller H, Hübner C, Mundlos S.

Am J Hum Genet. 2006 Aug;79(2):303-12. Epub 2006 Jun 20.

PubMed [citation]

PMID:: 16826520
PMCID:: PMC1559482

See all PubMed Citations (8)

Details of each submission

From GeneDx, SCV000329801.8

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

Description

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; This variant is associated with the following publications: (PMID: 25957469, 25608830, 30868735, 24038971, 22167768, 34426522, 31589614, 33250842, 32587836, 16826531)

#	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 Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001905677.1

#	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	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002019314.3

#	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

From Invitae, SCV003195503.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This sequence change creates a premature translational stop signal (p.Val253Alafs*44) in the CHRNG gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CHRNG are known to be pathogenic (PMID: 16826520). This variant is present in population databases (rs767503038, gnomAD 0.03%). This premature translational stop signal has been observed in individuals with lethal and Escobar variant multiple pterygium syndrome (PMID: 16826531, 22167768, 24038971, 25608830, 27245440). ClinVar contains an entry for this variant (Variation ID: 18342). 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: Jun 23, 2024

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