NM_000492.4(CFTR):c.3485G>T (p.Arg1162Leu) AND CFTR-related disorder

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Mar 26, 2018
Review status:: criteria provided, conflicting classifications

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:: RCV001009501.16

Allele description [Variation Report for NM_000492.4(CFTR):c.3485G>T (p.Arg1162Leu)]

NM_000492.4(CFTR):c.3485G>T (p.Arg1162Leu)

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.3485G>T (p.Arg1162Leu)

HGVS:

NC_000007.14:g.117627538G>T
NG_016465.4:g.166755G>T
NM_000492.4:c.3485G>TMANE SELECT
NP_000483.3:p.Arg1162Leu
NP_000483.3:p.Arg1162Leu
LRG_663t1:c.3485G>T
LRG_663:g.166755G>T
LRG_663p1:p.Arg1162Leu
NC_000007.13:g.117267592G>T
NM_000492.3:c.3485G>T
NM_000492.4:c.3485G>T
P13569:p.Arg1162Leu

Protein change:

R1162L

Links:

UniProtKB: P13569#VAR_000252; dbSNP: rs1800120

NCBI 1000 Genomes Browser:

rs1800120

Molecular consequence:

NM_000492.4:c.3485G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: CFTR-related disorder (CFTR-RD)
Synonyms:: CFTR-related disorders; CFTR-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001169596	CFTR-France	criteria provided, single submitter (Claustres M et al. (Hum Mutat 2017))	Pathogenic (Mar 26, 2018)	germline	curation	PubMed (1) [See all records that cite this PMID]
SCV001325860	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12167682, 18687795, 1379210 Citation Link,
SCV002029122	GenomeConnect, ClinGen	no classification provided	not provided	maternal	phenotyping only

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001169596

CFTR-France

criteria provided, single submitter

(Claustres M et al. (Hum Mutat 2017))

Pathogenic
(Mar 26, 2018)

germline

curation

PubMed (1)
[See all records that cite this PMID]

SCV001325860

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV002029122

GenomeConnect, ClinGen

no classification provided

not provided

maternal

phenotyping only

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	curation
not provided	maternal	unknown	not provided	not provided	not provided	not provided	not provided	phenotyping only
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	curation
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants.

Claustres M, Thèze C, des Georges M, Baux D, Girodon E, Bienvenu T, Audrezet MP, Dugueperoux I, Férec C, Lalau G, Pagin A, Kitzis A, Thoreau V, Gaston V, Bieth E, Malinge MC, Reboul MP, Fergelot P, Lemonnier L, Mekki C, Fanen P, Bergougnoux A, et al.

Hum Mutat. 2017 Oct;38(10):1297-1315. doi: 10.1002/humu.23276. Epub 2017 Jun 28.

PubMed [citation]

PMID:: 28603918

Variant cystic fibrosis phenotypes in the absence of CFTR mutations.

Groman JD, Meyer ME, Wilmott RW, Zeitlin PL, Cutting GR.

N Engl J Med. 2002 Aug 8;347(6):401-7.

PubMed [citation]

PMID:: 12167682

See all PubMed Citations (4)

Details of each submission

From CFTR-France, SCV001169596.1

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

#	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
2	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV001325860.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown 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

From GenomeConnect, ClinGen, SCV002029122.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	phenotyping only	not provided

Description

Variant interpreted as other and reported on 04-28-2016 by Lab or GTR ID 500110. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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

Last Updated: Oct 26, 2024

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