NM_000492.4(CFTR):c.293A>G (p.Gln98Arg) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 25, 2022
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:: RCV003476943.1

Allele description [Variation Report for NM_000492.4(CFTR):c.293A>G (p.Gln98Arg)]

NM_000492.4(CFTR):c.293A>G (p.Gln98Arg)

Gene:

CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000492.4(CFTR):c.293A>G (p.Gln98Arg)

HGVS:

NC_000007.14:g.117530918A>G
NG_016465.4:g.70135A>G
NM_000492.4:c.293A>GMANE SELECT
NP_000483.3:p.Gln98Arg
NP_000483.3:p.Gln98Arg
LRG_663t1:c.293A>G
LRG_663:g.70135A>G
LRG_663p1:p.Gln98Arg
NC_000007.13:g.117170972A>G
NM_000492.3:c.293A>G
P13569:p.Gln98Arg

Protein change:

Q98R

Links:

UniProtKB: P13569#VAR_000116; dbSNP: rs397508464

NCBI 1000 Genomes Browser:

rs397508464

Molecular consequence:

NM_000492.4:c.293A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004221680	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Pathogenic (Jun 25, 2022)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 29805046, 25580864, 23687349, 26467025
SCV004226566	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 20, 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

SCV004221680

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Pathogenic
(Jun 25, 2022)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004226566

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 20, 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	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity.

Raraigh KS, Han ST, Davis E, Evans TA, Pellicore MJ, McCague AF, Joynt AT, Lu Z, Atalar M, Sharma N, Sheridan MB, Sosnay PR, Cutting GR.

Am J Hum Genet. 2018 Jun 7;102(6):1062-1077. doi: 10.1016/j.ajhg.2018.04.003. Epub 2018 May 24.

PubMed [citation]

PMID:: 29805046
PMCID:: PMC5992123

Characterization of gene mutations and phenotypes of cystic fibrosis in Chinese patients.

Liu Y, Wang L, Tian X, Xu KF, Xu W, Li X, Yue C, Zhang P, Xiao Y, Zhang X.

Respirology. 2015 Feb;20(2):312-8. doi: 10.1111/resp.12452. Epub 2015 Jan 8.

PubMed [citation]

PMID:: 25580864

See all PubMed Citations (5)

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004221680.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

The frequency of this variant in the general population, 0.000008 (2/251054 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. In the published literature, the variant has been reported in several compound heterozygotes affected with cystic fibrosis (UMD (http://www.umd.be/), PMIDs: 25580864 (2015), 23687349 (2013)). Additionally, functional studies showed reduced chloride channel activity indicating that this variant impacts protein function (PMID: 29805046 (2018)). Based on the available information, this variant is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV004226566.1

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

Description

PP3, PM2, PM3_very_strong, PS3

#	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

Last Updated: Jun 17, 2024

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