NM_212482.4(FN1):c.3121C>A (p.Gln1041Lys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 27, 2022
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:: RCV002908868.3

Allele description [Variation Report for NM_212482.4(FN1):c.3121C>A (p.Gln1041Lys)]

NM_212482.4(FN1):c.3121C>A (p.Gln1041Lys)

Gene:

FN1:fibronectin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_212482.4(FN1):c.3121C>A (p.Gln1041Lys)

HGVS:

NC_000002.12:g.215404521G>T
NG_012196.1:g.36548C>A
NG_012196.2:g.36547C>A
NM_001306129.2:c.3121C>A
NM_001306130.2:c.3121C>A
NM_001306131.2:c.3121C>A
NM_001306132.2:c.3121C>A
NM_001365517.2:c.3121C>A
NM_001365518.2:c.3121C>A
NM_001365519.2:c.3121C>A
NM_001365520.2:c.3121C>A
NM_001365521.2:c.3121C>A
NM_001365522.2:c.3121C>A
NM_001365523.2:c.3121C>A
NM_001365524.2:c.3121C>A
NM_002026.4:c.3121C>A
NM_212474.3:c.3121C>A
NM_212476.3:c.3121C>A
NM_212478.3:c.3121C>A
NM_212482.4:c.3121C>AMANE SELECT
NP_001293058.2:p.Gln1041Lys
NP_001293059.2:p.Gln1041Lys
NP_001293060.2:p.Gln1041Lys
NP_001293061.2:p.Gln1041Lys
NP_001352446.1:p.Gln1041Lys
NP_001352447.1:p.Gln1041Lys
NP_001352448.1:p.Gln1041Lys
NP_001352449.1:p.Gln1041Lys
NP_001352450.1:p.Gln1041Lys
NP_001352451.1:p.Gln1041Lys
NP_001352452.1:p.Gln1041Lys
NP_001352453.1:p.Gln1041Lys
NP_002017.2:p.Gln1041Lys
NP_997639.2:p.Gln1041Lys
NP_997641.2:p.Gln1041Lys
NP_997643.2:p.Gln1041Lys
NP_997647.2:p.Gln1041Lys
NC_000002.11:g.216269244G>T

Protein change:

Q1041K

Molecular consequence:

NM_001306129.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001306130.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001306131.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001306132.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365517.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365518.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365519.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365520.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365521.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365522.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365523.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365524.2:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002026.4:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212474.3:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212476.3:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212478.3:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_212482.4:c.3121C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PREDICTED: Equus caballus HECT domain E3 ubiquitin protein ligase 1 (HECTD1), tr...
PREDICTED: Equus caballus HECT domain E3 ubiquitin protein ligase 1 (HECTD1), transcript variant X1, mRNA
gi|1333552712|ref|XM_001489863.6|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003253994	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 27, 2022)	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

SCV003253994

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 27, 2022)

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, SCV003253994.2

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

Description

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. 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. This variant has not been reported in the literature in individuals affected with FN1-related conditions. This variant is present in population databases (rs762963114, gnomAD 0.003%). This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 1041 of the FN1 protein (p.Gln1041Lys).

#	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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