NM_000492.4(CFTR):c.3897A>G (p.Thr1299=) AND CFTR-related disorder

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 27, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001158876.15

Allele description [Variation Report for NM_000492.4(CFTR):c.3897A>G (p.Thr1299=)]

NM_000492.4(CFTR):c.3897A>G (p.Thr1299=)

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.3897A>G (p.Thr1299=)

HGVS:

NC_000007.14:g.117652865A>G
NG_016465.4:g.192082A>G
NM_000492.4:c.3897A>GMANE SELECT
NP_000483.3:p.Thr1299=
NP_000483.3:p.Thr1299=
LRG_663t1:c.3897A>G
LRG_663:g.192082A>G
LRG_663p1:p.Thr1299=
NC_000007.13:g.117292919A>G
NM_000492.3:c.3897A>G
NP_000483.3:p.(=)
p.Thr1299Thr

Links:

dbSNP: rs1800131

NCBI 1000 Genomes Browser:

rs1800131

Molecular consequence:

NM_000492.4:c.3897A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

Recent activity

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GSM2385295[Accession] (4)
GEO DataSets
Stevia kuhnioides (7)
NLM Catalog
protein adenylyltransferase FICD [Mus musculus]
protein adenylyltransferase FICD [Mus musculus]
gi|169646312|ref|NP_001010825.2|

Protein
Homo sapiens thiosulfate sulfurtransferase like domain containing 3 (TSTD3), tra...
Homo sapiens thiosulfate sulfurtransferase like domain containing 3 (TSTD3), transcript variant 2, non-coding RNA
gi|2788421403|ref|NR_197367.1|

Nucleotide
MIMAG Metagenome-assembled Genome sample from Thermoplasmatota archaeon
MIMAG Metagenome-assembled Genome sample from Thermoplasmatota archaeon

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001320539	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 26911355, 26436105, 18687795, 23378595 Citation Link,
SCV002029153	Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals	no assertion criteria provided (ACMG Guidelines, 2015)	Likely benign (Mar 29, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002075908	Natera, Inc.	no assertion criteria provided	Likely benign (Mar 21, 2018)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001320539

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV002029153

Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals

no assertion criteria provided

(ACMG Guidelines, 2015)

Likely benign
(Mar 29, 2021)

germline

clinical testing

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

SCV002075908

Natera, Inc.

no assertion criteria provided

Likely benign
(Mar 21, 2018)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The novel complex allele [A238V;F508del] of the CFTR gene: clinical phenotype and possible implications for cystic fibrosis etiological therapies.

Diana A, Polizzi AM, Santostasi T, Ratclif L, Pantaleo MG, Leonetti G, Iusco DR, Gallo C, Conese M, Manca A.

J Hum Genet. 2016 Jun;61(6):473-81. doi: 10.1038/jhg.2016.15. Epub 2016 Feb 25.

PubMed [citation]

PMID:: 26911355

Validation of a semiconductor next-generation sequencing assay for the clinical genetic screening of CFTR.

Trujillano D, Weiss ME, Köster J, Papachristos EB, Werber M, Kandaswamy KK, Marais A, Eichler S, Creed J, Baysal E, Jaber IY, Mehaney DA, Farra C, Rolfs A.

Mol Genet Genomic Med. 2015 Sep;3(5):396-403. doi: 10.1002/mgg3.149. Epub 2015 Apr 16.

PubMed [citation]

PMID:: 26436105
PMCID:: PMC4585447

See all PubMed Citations (5)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001320539.1

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

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 Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals, SCV002029153.1

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

From Natera, Inc., SCV002075908.1

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

#	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

Last Updated: Nov 10, 2024

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