ClinVar Genomic variation as it relates to human health
NM_000492.4(CFTR):c.2T>C (p.Met1Thr)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000492.4(CFTR):c.2T>C (p.Met1Thr)
Variation ID: 53622 Accession: VCV000053622.37
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7q31.2 7: 117480096 (GRCh38) [ NCBI UCSC ] 7: 117120150 (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 Mar 29, 2015 Oct 8, 2024 Nov 17, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000492.4:c.2T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000483.3:p.Met1Thr missense initiator codon variant NC_000007.14:g.117480096T>C NC_000007.13:g.117120150T>C NG_016465.4:g.19313T>C NG_056120.2:g.4126T>C LRG_663:g.19313T>C LRG_663t1:c.2T>C LRG_663p1:p.Met1Thr - Protein change
- M1T
- Other names
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- Canonical SPDI
- NC_000007.14:117480095: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
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
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
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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 |
3835 | 5214 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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/Likely pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Nov 17, 2023 | RCV000046751.18 | |
Pathogenic (1) |
criteria provided, single submitter
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- | RCV002262607.3 | |
Pathogenic (2) |
no assertion criteria provided
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Feb 21, 2024 | RCV001826652.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 29, 2022 | RCV002477157.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 3, 2023 | RCV003476944.1 |
Submissions - Germline
Classification
Help
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
Help
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
Help
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
(-)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Lifecell International Pvt. Ltd
Accession: SCV003853258.2
First in ClinVar: Apr 09, 2023 Last updated: Sep 03, 2023 |
Comment:
A Heterozygous Start lost variant c.2T>C in Exon 1 of the CFTR gene that results in the amino acid substitution p.Met1? was identified. The observed … (more)
A Heterozygous Start lost variant c.2T>C in Exon 1 of the CFTR gene that results in the amino acid substitution p.Met1? was identified. The observed variant has a minor allele frequency of 0.00001 and novel in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic/ Likely Pathogenic (Variant ID: 53622). This alteration has been reported in individuals with cystic fibrosis (Bienvenu T et al. 2005). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. (less)
Zygosity: Compound Heterozygote
Ethnicity/Population group: Asian
Geographic origin: India
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Pathogenic
(Aug 03, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004221681.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
The CFTR c.2T>C variant disrupts the translation initiation codon of the CFTR mRNA and is predicted to interfere with CFTR protein synthesis. This variant has … (more)
The CFTR c.2T>C variant disrupts the translation initiation codon of the CFTR mRNA and is predicted to interfere with CFTR protein synthesis. This variant has been reported in the published literature in individuals with cystic fibrosis (PMID: 16596947 (2005), 16436643 (2006), 19910674 (2009), 22299590 (2012), 27086061(2016)). Published functional studies showed that truncated CFTR protein produced due to downstream alternate start codons had reduced stability and reduced chloride channel activity (PMID: 19910674 (2009)). The frequency of this variant in the general population, 0.000008 (2/251170 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Oct 02, 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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Ambry Genetics
Accession: SCV002748827.3
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.M1? pathogenic mutation (also known as c.2T>C) is located in coding exon 1 of the CFTR gene and results from a T to C … (more)
The p.M1? pathogenic mutation (also known as c.2T>C) is located in coding exon 1 of the CFTR gene and results from a T to C substitution at nucleotide position 2. This alters the methionine residue at the initiation codon (ATG). This mutation has been reported in individuals with cystic fibrosis who had a second disease-causing variant (Bienvenu T et al. Hum. Biol., 2005 Oct;77:705-14; Gaitch N et al. Pancreatology Apr;16:515-22). Another alteration at the same codon, p.M1? (c.1A>G), has been reported in individuals with cystic fibrosis and CFTR-related disorders and shown to reduce CFTR function in vitro (des Georges M et al. J. Cyst. Fibros., 2004 Dec;3:265-72; Steiner B et al. Hum. Mutat., 2011 Aug;32:912-20; Sosnay PR et al. Nat. Genet., 2013 Oct;45:1160-7; Van Goor F et al. J. Cyst. Fibros., 2014 Jan;13:29-36). In addition to the clinical data presented in the literature, sequence variations that modify the initiation codon are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Jan 29, 2018)
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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: SCV001169260.2
First in ClinVar: Mar 16, 2020 Last updated: Sep 03, 2023 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Congenital bilateral aplasia of vas deferens from CFTR mutation
Cystic fibrosis (Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
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Suma Genomics
Accession: SCV002543781.2
First in ClinVar: Jul 09, 2022 Last updated: Sep 03, 2023 |
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Pathogenic
(Feb 01, 2013)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: yes
Allele origin:
germline
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Arcensus
Accession: SCV002564627.2
First in ClinVar: Dec 17, 2022 Last updated: Sep 03, 2023 |
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Likely pathogenic
(Jul 23, 2014)
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criteria provided, single submitter
Method: literature only
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Cystic fibrosis
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000220549.3
First in ClinVar: Mar 29, 2015 Last updated: Sep 03, 2023 |
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Pathogenic
(Mar 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary pancreatitis
Bronchiectasis with or without elevated sweat chloride 1 Cystic fibrosis Congenital bilateral aplasia of vas deferens from CFTR mutation
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002794986.2
First in ClinVar: Dec 31, 2022 Last updated: Sep 03, 2023 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Cystic fibrosis
Affected status: yes
Allele origin:
germline
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Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
Accession: SCV004030493.1
First in ClinVar: Sep 03, 2023 Last updated: Sep 03, 2023 |
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Pathogenic
(Nov 17, 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: SCV001591502.5
First in ClinVar: May 10, 2021 Last updated: Feb 20, 2024 |
Comment:
This sequence change affects the initiator methionine of the CFTR mRNA. The next in-frame methionine is located at codon 82. This variant is present in … (more)
This sequence change affects the initiator methionine of the CFTR mRNA. The next in-frame methionine is located at codon 82. This variant is present in population databases (rs397508476, gnomAD 0.006%). Disruption of the initiator codon has been observed in individual(s) with cystic fibrosis (PMID: 22299590, 27086061). This variant is also known as 134T>C; p.M1T. ClinVar contains an entry for this variant (Variation ID: 53622). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jul 20, 2021)
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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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Natera, Inc.
Accession: SCV002080054.2
First in ClinVar: Feb 13, 2022 Last updated: Sep 03, 2023 |
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Pathogenic
(Feb 21, 2024)
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no assertion criteria provided
Method: clinical testing
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CFTR-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004717679.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The CFTR c.2T>C variant is predicted to disrupt the translation initiation site (Start Loss). The c.2T>C variant (also known as c.134T>C in the literature) has … (more)
The CFTR c.2T>C variant is predicted to disrupt the translation initiation site (Start Loss). The c.2T>C variant (also known as c.134T>C in the literature) has been reported to be causative for CFTR-related disorders (Bienvenu et al. 2005. PubMed ID: 16596947; Elahi et al. 2006. PubMed ID: 16436643; Sachdeva et al. 2012. PubMed ID: 22299590; http://www.genet.sickkids.on.ca). This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD. Similar variants affecting the consensus start codon (c.1A>G, c.2T>A, c.3G>A, and c.3G>T) have also been reported in patients with cystic fibrosis (Human Gene Mutation Database, http://www.hgmd.cf.ac.uk/). This variant is interpreted as pathogenic. (less)
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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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CFTR and/or pancreatitis susceptibility genes mutations as risk factors of pancreatitis in cystic fibrosis patients? | Gaitch N | Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] | 2016 | PMID: 27086061 |
Effect of ivacaftor on CFTR forms with missense mutations associated with defects in protein processing or function. | Van Goor F | Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society | 2014 | PMID: 23891399 |
Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. | Sosnay PR | Nature genetics | 2013 | PMID: 23974870 |
Mutation analysis of the CFTR gene in 225 children: identification of five novel severe and seven reported severe mutations. | Sachdeva K | Genetic testing and molecular biomarkers | 2012 | PMID: 22299590 |
Common CFTR haplotypes and susceptibility to chronic pancreatitis and congenital bilateral absence of the vas deferens. | Steiner B | Human mutation | 2011 | PMID: 21520337 |
Deletion of CFTR translation start site reveals functional isoforms of the protein in CF patients. | Ramalho AS | Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology | 2009 | PMID: 19910674 |
A haplotype framework for cystic fibrosis mutations in Iran. | Elahi E | The Journal of molecular diagnostics : JMD | 2006 | PMID: 16436643 |
Spectrum of CFTR mutations on Réunion Island: impact on neonatal screening. | Bienvenu T | Human biology | 2005 | PMID: 16596947 |
Malnutrition in adults with cystic fibrosis. | Dray X | European journal of clinical nutrition | 2005 | PMID: 15367921 |
High heterogeneity of CFTR mutations and unexpected low incidence of cystic fibrosis in the Mediterranean France. | des Georges M | Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society | 2004 | PMID: 15698946 |
Alternate translation initiation codons can create functional forms of cystic fibrosis transmembrane conductance regulator. | Carroll TP | The Journal of biological chemistry | 1995 | PMID: 7538127 |
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Text-mined citations for rs397508476 ...
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.