NM_000492.4(CFTR):c.260T>C (p.Phe87Ser) AND Cystic fibrosis

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Nov 5, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001216825.19

Allele description [Variation Report for NM_000492.4(CFTR):c.260T>C (p.Phe87Ser)]

NM_000492.4(CFTR):c.260T>C (p.Phe87Ser)

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.260T>C (p.Phe87Ser)

HGVS:

NC_000007.14:g.117509129T>C
NG_016465.4:g.48346T>C
NG_062452.1:g.767T>C
NM_000492.4:c.260T>CMANE SELECT
NP_000483.3:p.Phe87Ser
LRG_663t1:c.260T>C
LRG_663:g.48346T>C
NC_000007.13:g.117149183T>C
NM_000492.3:c.260T>C

Protein change:

F87S

Links:

dbSNP: rs1310658028

NCBI 1000 Genomes Browser:

rs1310658028

Molecular consequence:

NM_000492.4:c.260T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cystic fibrosis (CF)
Synonyms:: Mucoviscidosis
Identifiers:: MONDO: MONDO:0009061; MedGen: C0010674; Orphanet: 586; OMIM: 219700

Recent activity

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PREDICTED: Nasonia vitripennis alpha-1,3/1,6-mannosyltransferase ALG2 (LOC100122...
PREDICTED: Nasonia vitripennis alpha-1,3/1,6-mannosyltransferase ALG2 (LOC100122589), mRNA
gi|1815736984|ref|XM_001607260.6|

Nucleotide
dnaJ homolog subfamily B member 2 isoform X1 [Bactrocera oleae]
dnaJ homolog subfamily B member 2 isoform X1 [Bactrocera oleae]
gi|1912037984|ref|XP_036224988.1|

Protein
PREDICTED: beta-galactoside alpha-2,6-sialyltransferase 2 isoform X1 [Thamnophis...
PREDICTED: beta-galactoside alpha-2,6-sialyltransferase 2 isoform X1 [Thamnophis sirtalis]
gi|927133921|ref|XP_013910859.1|

Protein
Mus musculus guanine nucleotide binding protein (G protein), gamma 8 (Gng8), tra...
Mus musculus guanine nucleotide binding protein (G protein), gamma 8 (Gng8), transcript variant 3, mRNA
gi|2311615199|ref|NM_001412472.1|

Nucleotide
guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-8 [Mus musculus]
guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-8 [Mus musculus]
gi|2311615213|ref|NP_001399405.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001388638	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 8081395, 19181743, 28492532
SCV002027338	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002745557	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 5, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001388638

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

germline

clinical testing

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

SCV002027338

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 5, 2021)

germline

clinical testing

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

SCV002745557

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 5, 2023)

germline

clinical testing

Citation Link

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	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A missense mutation (F87L) in exon 3 of the cystic fibrosis transmembrane conductance regulator gene.

Bienvenu T, Petitpretz P, Beldjord C, Kaplan JC.

Hum Mutat. 1994;3(4):395-6. No abstract available.

PubMed [citation]

PMID:: 8081395

Heterogenous spectrum of CFTR gene mutations in Indian patients with congenital absence of vas deferens.

Sharma N, Acharya N, Singh SK, Singh M, Sharma U, Prasad R.

Hum Reprod. 2009 May;24(5):1229-36. doi: 10.1093/humrep/den500. Epub 2009 Jan 30.

PubMed [citation]

PMID:: 19181743

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001388638.4

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

Description

This sequence change replaces phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 87 of the CFTR protein (p.Phe87Ser). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with CFTR-related conditions. ClinVar contains an entry for this variant (Variation ID: 946044). 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 not expected to disrupt CFTR protein function. This variant disrupts the p.Phe87 amino acid residue in CFTR. Other variant(s) that disrupt this residue have been observed in individuals with CFTR-related conditions (PMID: 8081395, 19181743), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain 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 Genome-Nilou Lab, SCV002027338.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Ambry Genetics, SCV002745557.2

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

Description

The p.F87S variant (also known as c.260T>C), located in coding exon 3 of the CFTR gene, results from a T to C substitution at nucleotide position 260. The phenylalanine at codon 87 is replaced by serine, an amino acid with highly dissimilar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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