NM_212482.4(FN1):c.1757A>G (p.Gln586Arg) AND Glomerulopathy with fibronectin deposits 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 1, 2019
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:: RCV001007576.1

Allele description [Variation Report for NM_212482.4(FN1):c.1757A>G (p.Gln586Arg)]

NM_212482.4(FN1):c.1757A>G (p.Gln586Arg)

Gene:

FN1:fibronectin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_212482.4(FN1):c.1757A>G (p.Gln586Arg)

HGVS:

NC_000002.12:g.215419304T>C
NG_012196.1:g.21765A>G
NM_001306129.2:c.1757A>G
NM_001306130.2:c.1757A>G
NM_001306131.2:c.1757A>G
NM_001306132.2:c.1757A>G
NM_001365517.2:c.1757A>G
NM_001365518.2:c.1757A>G
NM_001365519.2:c.1757A>G
NM_001365520.2:c.1757A>G
NM_001365521.2:c.1757A>G
NM_001365522.2:c.1757A>G
NM_001365523.2:c.1757A>G
NM_001365524.2:c.1757A>G
NM_002026.4:c.1757A>G
NM_054034.3:c.1757A>G
NM_212474.3:c.1757A>G
NM_212476.3:c.1757A>G
NM_212478.3:c.1757A>G
NM_212482.4:c.1757A>GMANE SELECT
NP_001293058.2:p.Gln586Arg
NP_001293059.2:p.Gln586Arg
NP_001293060.2:p.Gln586Arg
NP_001293061.2:p.Gln586Arg
NP_001352446.1:p.Gln586Arg
NP_001352447.1:p.Gln586Arg
NP_001352448.1:p.Gln586Arg
NP_001352449.1:p.Gln586Arg
NP_001352450.1:p.Gln586Arg
NP_001352451.1:p.Gln586Arg
NP_001352452.1:p.Gln586Arg
NP_001352453.1:p.Gln586Arg
NP_002017.2:p.Gln586Arg
NP_473375.2:p.Gln586Arg
NP_997639.2:p.Gln586Arg
NP_997641.2:p.Gln586Arg
NP_997643.2:p.Gln586Arg
NP_997647.2:p.Gln586Arg
NC_000002.11:g.216284027T>C
NC_000002.11:g.216284027T>C
NM_212482.2:c.1757A>G

Protein change:

Q586R

Links:

dbSNP: rs138219703

NCBI 1000 Genomes Browser:

rs138219703

Molecular consequence:

NM_001306129.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001306130.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001306131.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001306132.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365517.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365518.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365519.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365520.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365521.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365522.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365523.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365524.2:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002026.4:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_054034.3:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_212474.3:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_212476.3:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_212478.3:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_212482.4:c.1757A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glomerulopathy with fibronectin deposits 2 (GFND2)
Synonyms:: Glomerular nephritis familial with fibronectin deposits
Identifiers:: MONDO: MONDO:0011165; MedGen: C1866075; Orphanet: 84090; OMIM: 601894

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001167205	Johns Hopkins Genomics, Johns Hopkins University	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 1, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001167205

Johns Hopkins Genomics, Johns Hopkins University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 1, 2019)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Johns Hopkins Genomics, Johns Hopkins University, SCV001167205.1

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

Description

This FN1 variant (rs138219703) is present in a large population datasets (gnomAD: 9/282834 total alleles; 0.0032%; no homozygotes). FN1 c.1757A>G has not been reported in ClinVar nor the literature, to our knowledge. Of two bioinformatics tools queried, one predicts that the substitution would be probably damaging, while the second predicts that it would be tolerated. The glutamine residue at this position is highly evolutionarily conserved across most species assessed. The clinical significance of c.1757A>G is uncertain at this time.

#	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: Sep 29, 2024

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