Updates for c.3896C>T:
2015-07-01 class changed from disease-causing to unclassified
2024-10-14 Class updated from VUS4 to likely pathogenic/likely CFTR-RD




Variant NM_000492.4:c.3896C>T


Variant details:
Name NM_000492.4:c.3896C>T
Protein name NP_000483.3:p.(Thr1299Ile)
Genomic name (hg19)     chr7:g.117292918C>T    UCSC    
Genomic name (hg38) chr7:g.117652864C>T    UCSC
#Exon/intron exon 24
Legacy Name T1299I
Class likely pathogenic
Subclass likely CFTR-RD
WT sequence TAGAAAGTATTTATTTTTTCTGGAA C ATTTAGAAAAAACTTGGATCCCTAT
Mutant sequence TAGAAAGTATTTATTTTTTCTGGAA T ATTTAGAAAAAACTTGGATCCCTAT

Other databases:

Not found		dbSNP
rs397508634



Pathogenicity predictors:



Response to modulators:


Modulator FDA approval EMA approval in vitro / ex vivo data clinical data
ELX-TEZ-IVA yesnoyesno
VNZ-TEZ-DIVA yesnoyesno

clinical and functional data presented above are provided by Vertex


No patient found in CFTR-NGS catalogue


3 patients carrying this variant are reported in CFTR-France:

TOTAL NUMBER OF PATIENTS 3
CF 1
CFTR-RD2
  • Bronchiectasis  1
  • Other  1




Color code:   non disease-causing <   likely benign <   VUS <   likely pathogenic <   disease-causing

Detailed genotypes:
Phenotype Patient ID Variant status Additional variants
Bronchiectasis 1905heterozygoteCF-causing- Undef
Other 4884heterozygoteCF-causing- Undef
CF 4386heterozygote


Color code:   non disease-causing <   likely benign <   VUS <   likely pathogenic <   disease-causing



            CFTR variants are clustered into five groups (click here for more details about the classification of variants):
  • CF-causing: when in trans with another CF-causing mutation, will result in CF.
  • CFTR-RD causing: when in trans with a CF-causing mutation, will result in CFTR-related disorders (CFTR-RD) such as chronic pancreatitis, bronchiectasis, CRS-NP (chronic rhinosinusitis with or without nasal polyposis) or CBAVD (congenital absence of vas deferens), according to Bombieri C et al., 2011.
  • Varying clinical consequence: when in trans with another CF-causing mutation, can either result in CF or in a CFTR-RD.
  • Non disease-causing: when in trans with a CF-causing mutation, will not cause CF, nor CFTR-RD.
  • VUS (Variant of unknown clinical significance): unclassified because of insufficient data.



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