NM_212482.4(FN1):c.3062G>A (p.Arg1021Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 25, 2023
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:: RCV001306363.7

Allele description [Variation Report for NM_212482.4(FN1):c.3062G>A (p.Arg1021Gln)]

NM_212482.4(FN1):c.3062G>A (p.Arg1021Gln)

Gene:

FN1:fibronectin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_212482.4(FN1):c.3062G>A (p.Arg1021Gln)

HGVS:

NC_000002.12:g.215404580C>T
NG_012196.1:g.36489G>A
NM_001306129.2:c.3062G>A
NM_001306130.2:c.3062G>A
NM_001306131.2:c.3062G>A
NM_001306132.2:c.3062G>A
NM_001365517.2:c.3062G>A
NM_001365518.2:c.3062G>A
NM_001365519.2:c.3062G>A
NM_001365520.2:c.3062G>A
NM_001365521.2:c.3062G>A
NM_001365522.2:c.3062G>A
NM_001365523.2:c.3062G>A
NM_001365524.2:c.3062G>A
NM_002026.4:c.3062G>A
NM_212474.3:c.3062G>A
NM_212476.3:c.3062G>A
NM_212478.3:c.3062G>A
NM_212482.2:c.3062G>A
NM_212482.4:c.3062G>AMANE SELECT
NP_001293058.2:p.Arg1021Gln
NP_001293059.2:p.Arg1021Gln
NP_001293060.2:p.Arg1021Gln
NP_001293061.2:p.Arg1021Gln
NP_001352446.1:p.Arg1021Gln
NP_001352447.1:p.Arg1021Gln
NP_001352448.1:p.Arg1021Gln
NP_001352449.1:p.Arg1021Gln
NP_001352450.1:p.Arg1021Gln
NP_001352451.1:p.Arg1021Gln
NP_001352452.1:p.Arg1021Gln
NP_001352453.1:p.Arg1021Gln
NP_002017.2:p.Arg1021Gln
NP_997639.2:p.Arg1021Gln
NP_997641.2:p.Arg1021Gln
NP_997643.2:p.Arg1021Gln
NP_997647.2:p.Arg1021Gln
NC_000002.11:g.216269303C>T

Protein change:

R1021Q

Links:

dbSNP: rs139603893

NCBI 1000 Genomes Browser:

rs139603893

Molecular consequence:

NM_001306129.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001306130.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001306131.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001306132.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365517.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365518.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365519.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365520.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365521.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365522.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365523.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365524.2:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002026.4:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212474.3:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212476.3:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212478.3:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212482.4:c.3062G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Caldithrix abyssi DSM 13497
Caldithrix abyssi DSM 13497
Caldithrix abyssi DSM 13497 genome sequencing project

BioProject
BBD41_RS29625 [Paenibacillus ihbetae]
BBD41_RS29625 [Paenibacillus ihbetae]
Gene ID:48312405

Gene
BBD41_RS27650 [Paenibacillus ihbetae]
BBD41_RS27650 [Paenibacillus ihbetae]
Gene ID:48312025

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001495733	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 25, 2023)	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

SCV001495733

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 25, 2023)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001495733.4

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1021 of the FN1 protein (p.Arg1021Gln). This variant is present in population databases (rs139603893, gnomAD 0.02%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with FN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1008946). 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 FN1 protein function with a negative predictive value of 80%. 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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine