ClinVar Genomic variation as it relates to human health
NM_000492.4(CFTR):c.4004T>C (p.Leu1335Pro)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000492.4(CFTR):c.4004T>C (p.Leu1335Pro)
Variation ID: 53872 Accession: VCV000053872.22
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7q31.2 7: 117664728 (GRCh38) [ NCBI UCSC ] 7: 117304782 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 6, 2016 Jul 15, 2024 Dec 8, 2017 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000492.4:c.4004T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000483.3:p.Leu1335Pro missense NC_000007.14:g.117664728T>C NC_000007.13:g.117304782T>C NG_016465.4:g.203945T>C LRG_663:g.203945T>C LRG_663t1:c.4004T>C LRG_663p1:p.Leu1335Pro - Protein change
- L1335P
- Other names
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- Canonical SPDI
- NC_000007.14:117664727:T:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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CFTR | - | - |
GRCh38 GRCh37 |
3832 | 5210 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (10) |
reviewed by expert panel
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Dec 8, 2017 | RCV000047055.25 | |
Pathogenic (1) |
no assertion criteria provided
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Jul 23, 2019 | RCV002228162.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 2, 2023 | RCV003474598.1 |
Submissions - Germline
Classification
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The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Dec 08, 2017)
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reviewed by expert panel
Method: research
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Cystic fibrosis
Affected status: yes
Allele origin:
germline
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CFTR2
Accession: SCV000924276.1
First in ClinVar: Jun 17, 2019 Last updated: Jun 17, 2019 |
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Uncertain significance
(Jul 27, 2016)
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criteria provided, single submitter
Method: clinical testing
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CFTR-Related Disorders
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000466527.3
First in ClinVar: Dec 06, 2016 Last updated: May 27, 2019 |
Comment:
The CFTR c.4004T>C (p.Leu1335Pro) variant is a missense variant that has been reported in four studies, where it was found in a heterozygous state in … (more)
The CFTR c.4004T>C (p.Leu1335Pro) variant is a missense variant that has been reported in four studies, where it was found in a heterozygous state in a total of six individuals with cystic fibrosis; no second variant was identified in these individuals (Scotet et al. 2003; Krenkova et al. 2009; Dorfman et al. 2010; Krenkova et al. 2013). Control data are unavailable for the p.Leu1335Pro variant, which is not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium despite being found in a region of good sequencing coverage. The variant is thus presumed to be rare. The evidence for this variant is limited. Therefore, the p.Leu1335Pro variant is classified as a variant of unknown significance but suspicious for pathogenicity for CFTR-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Pathogenic
(Jul 23, 2019)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: unknown
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002507325.1
First in ClinVar: May 16, 2022 Last updated: May 16, 2022 |
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Pathogenic
(Mar 06, 2020)
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criteria provided, single submitter
Method: curation
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Cystic fibrosis
Affected status: yes
Allele origin:
germline
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CFTR-France
Accession: SCV002573593.1
First in ClinVar: Sep 24, 2022 Last updated: Sep 24, 2022 |
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Pathogenic
(Aug 02, 2023)
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criteria provided, single submitter
Method: clinical testing
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Bronchiectasis with or without elevated sweat chloride 1
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004213442.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Jan 08, 2020)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002624522.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.L1335P pathogenic mutation (also known as c.4004T>C), located in coding exon 25 of the CFTR gene, results from a T to C substitution at … (more)
The p.L1335P pathogenic mutation (also known as c.4004T>C), located in coding exon 25 of the CFTR gene, results from a T to C substitution at nucleotide position 4004. The leucine at codon 1335 is replaced by proline, an amino acid with similar properties. This mutation was identified in two pancreatic sufficient individuals with cystic fibrosis (CF) in conjunction with p.F508del (Rose JB et al. Clin. Biochem., 2009 Aug;42:1260-4; Ivanov M et al. BMC Med Genomics, 2018 02;11:13). It has also been reported in cohorts of individuals with CF; however, specific genotype and phenotype information was not provided (Scotet V et al. Hum. Mutat., 2003 Jul;22:105; Ahmed N et al. Gut, 2003 Aug;52:1159-64; Kenková P et al. J. Cyst. Fibros., 2013 Sep;12:532-7). Functional analysis of this variant in CFBE cells demonstrated 2% activity compared to wild type (Raraigh KS et al. Am. J. Hum. Genet., 2018 06;102:1062-1077). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Apr 10, 2024)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919159.2
First in ClinVar: Jun 02, 2019 Last updated: Jul 15, 2024 |
Comment:
Variant summary: CFTR c.4004T>C (p.Leu1335Pro) results in a non-conservative amino acid change located in the ABC transporter-like domain (IPR003439) and AAA+ ATPase domains of the … (more)
Variant summary: CFTR c.4004T>C (p.Leu1335Pro) results in a non-conservative amino acid change located in the ABC transporter-like domain (IPR003439) and AAA+ ATPase domains of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251130 control chromosomes (gnomAD). c.4004T>C has been reported in the literature in multiple individuals affected with Cystic Fibrosis (e.g. Rose_2009, Masica_2015, Ivanov_2018, McCague_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant results in a loss of CFTR function (Han_2018). The following publications have been ascertained in the context of this evaluation (PMID: 12815607, 20059485, 15390350, 20163773, 20932301, 23276700, 25489051, 19445912, 29504914, 19734129, 30888834, 30046002). ClinVar contains an entry for this variant (Variation ID: 53872). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(May 29, 2018)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000800815.1
First in ClinVar: Dec 12, 2017 Last updated: Dec 12, 2017 |
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Likely pathogenic
(Sep 05, 2022)
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criteria provided, single submitter
Method: curation
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Cystic fibrosis
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV002574092.1
First in ClinVar: Sep 24, 2022 Last updated: Sep 24, 2022 |
Comment:
This variant was identified in 3 unrelated patients with a clinically confirmed diagnosis of cystic fibrosis. The variant was classified in the context of a … (more)
This variant was identified in 3 unrelated patients with a clinically confirmed diagnosis of cystic fibrosis. The variant was classified in the context of a project re-classifying variants in the German Cystic Fibrosis Registry (Muko.e.V.). Link: https://www.muko.info/angebote/qualitaetsmanagement/register/cf-einrichtungen/mukoweb. Criteria applied: PS3_SUP, PM2_SUP, PM3_STR, PM5, PP3 (less)
Number of individuals with the variant: 3
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Pathogenic
(Sep 03, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001587413.5
First in ClinVar: May 10, 2021 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 1335 of the CFTR protein (p.Leu1335Pro). … (more)
This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 1335 of the CFTR protein (p.Leu1335Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with cystic fibrosis (PMID: 19445912, 23974870, 29504914). ClinVar contains an entry for this variant (Variation ID: 53872). 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 CFTR protein function. Experimental studies have shown that this missense change affects CFTR function (PMID: 29805046). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Cystic Fibrosis
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001454291.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(Jul 23, 2019)
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no assertion criteria provided
Method: clinical testing
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CFTR-related disorders
Affected status: unknown
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002507409.1
First in ClinVar: May 16, 2022 Last updated: May 16, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Correlating Cystic Fibrosis Transmembrane Conductance Regulator Function with Clinical Features to Inform Precision Treatment of Cystic Fibrosis. | McCague AF | American journal of respiratory and critical care medicine | 2019 | PMID: 30888834 |
Residual function of cystic fibrosis mutants predicts response to small molecule CFTR modulators. | Han ST | JCI insight | 2018 | PMID: 30046002 |
Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. | Raraigh KS | American journal of human genetics | 2018 | PMID: 29805046 |
Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis. | Ivanov M | BMC medical genomics | 2018 | PMID: 29504914 |
Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. | Masica DL | Human molecular genetics | 2015 | PMID: 25489051 |
Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. | Sosnay PR | Nature genetics | 2013 | PMID: 23974870 |
Distribution of CFTR mutations in the Czech population: positive impact of integrated clinical and laboratory expertise, detection of novel/de novo alleles and relevance for related/derived populations. | Křenková P | Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society | 2013 | PMID: 23276700 |
Mutations that permit residual CFTR function delay acquisition of multiple respiratory pathogens in CF patients. | Green DM | Respiratory research | 2010 | PMID: 20932301 |
Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? | Dorfman R | Clinical genetics | 2010 | PMID: 20059485 |
Evaluation of high-resolution melting (HRM) for mutation scanning of selected exons of the CFTR gene. | Krenková P | Folia biologica | 2009 | PMID: 20163773 |
Sweat gland bioelectrics differ in cystic fibrosis: a new concept for potential diagnosis and assessment of CFTR function in cystic fibrosis. | Gonska T | Thorax | 2009 | PMID: 19734129 |
Does the Macroduct collection system reliably define sweat chloride concentration in subjects with intermediate results? | Rose JB | Clinical biochemistry | 2009 | PMID: 19445912 |
Dornase alpha and exhaled NO in cystic fibrosis. | Grasemann H | Pediatric pulmonology | 2004 | PMID: 15390350 |
Molecular consequences of cystic fibrosis transmembrane regulator (CFTR) gene mutations in the exocrine pancreas. | Ahmed N | Gut | 2003 | PMID: 12865275 |
Comparison of the CFTR mutation spectrum in three cohorts of patients of Celtic origin from Brittany (France) and Ireland. | Scotet V | Human mutation | 2003 | PMID: 12815607 |
https://cftr2.org | - | - | - | - |
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Text-mined citations for rs397508658 ...
HelpRecord last updated Nov 25, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.