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Primary immunodeficiency

Gene: FCN3

Red List (low evidence)

FCN3 (ficolin 3)
EnsemblGeneIds (GRCh38): ENSG00000142748
EnsemblGeneIds (GRCh37): ENSG00000142748
OMIM: 604973, Gene2Phenotype
FCN3 is in 3 panels

2 reviews

Sophie Hambleton (Newcastle University)

Red List (low evidence)

Probably not suitable for straightforward diagnostic reporting process
Created: 29 Jun 2018, 2:08 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

Zornitza Stark (VCGS) , pers. comm. notes there are multiple cases reported, but single variant, and rates the gene Green. However, as highlighted by previous expert review it is not suitable for straightforward diagnostic reporting process, further evidence is needed since the consequences of FCN3 deficiency do not seem to be not clear-cut, and it has been suggested that it may act as a disease modifier.
Created: 21 Sep 2018, 12:20 p.m.
Comment on list classification: Changed from Amber to Red due to Red review from external expert, agreeing this gene for straightforward diagnostic reporting process. To be referred back to Victorian Clinical Genetics Services for evidences.
Created: 4 Jul 2018, 10:01 a.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): FCN3 .PanelApp HGNC gene symbol check: FCN3 . IUIS Disease: Ficolin 3 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Respiratory infections, abscesses. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A
Created: 2 Jul 2018, 10:35 a.m.
Keep Amber until more info on gene and disease association, refer to external expert review. Only one variant reported to date, Michalski et al. (2012) PMID: 22226667 concluded that heterozygosity for the FCN3 variant does not seem to have major clinical importance PMID: 25662573, then in 2015 Michalski et al. PMID: 25662573 concluded that the consequences of FCN3 deficiency are not clear-cut, and suggested that it may act as a disease modifier.
Created: 19 Jun 2018, 10:46 a.m.
from PMID: 25662573, 19535802, Orphanet Immunodeficiency due to ficolin3 deficiency is a rare, genetic, immunodeficiency due to a complement cascade protein anomaly characterized by low or undetectable serum ficolin3 levels, susceptibility to infections, and possibly autoimmunity. The presentation is variable, from perinatal necrotizing enterocolitis and recurrent skin infections with Staphylococcus aureus to childhood-onset recurrent pulmonary infections leading to brain abscesses and pulmonary fibrosis, to membranous nephropathy. In some patients, clinical consequences of ficolin3 deficiency were not clear.
Created: 19 Jun 2018, 10:39 a.m.
Comment on publications: added publications to support the phenotype
Created: 19 Jun 2018, 10:39 a.m.
Comment on mode of inheritance: added MOI from PMID: 20971976
Created: 19 Jun 2018, 10:36 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: FCN3, PanelApp HGNC gene symbol check: FCN3, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Complement deficiencies / Complement deficiency / Ficolin3 deficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: FCN3, GRID_Gene_Symbol: FCN3, GRID_Transcript_ENS_Community submitted: ENST00000270879, GRID_Transcript_RefSeq: NM_003665.2, GRID_Transcript_ENS_used_on_Production: ENST00000270879
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • IUIS Classification December 2019
  • Expert Review Red
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Respiratory infections, abscesses
  • Immunodeficiency due to ficolin 3 deficiency, 613860
  • Complement Deficiencies
  • Ficolin3 deficiency
OMIM
604973
Clinvar variants
Variants in FCN3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Feb 2020, Gel status: 1

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to FCN3. Added phenotypes Respiratory infections, abscesses for gene: FCN3 Publications for gene FCN3 were updated from 19535802; 20971976; 22226667; 25662573 to 22226667; 32048120; 20971976; 19535802; 25662573; 32086639

12 Jul 2018, Gel status: 1

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: fcn3 has been classified as Red List (Low Evidence).

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: fcn3 has been classified as Red List (Low Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene FCN3 were set to Immunodeficiency due to ficolin 3 deficiency, 613860, Ficolin3 deficiency, Respiratory infections, abscesses, Complement Deficiencies

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to FCN3. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to FCN3. Panel: Primary immunodeficiency disorders

19 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: FCN3 were set to 19535802; 20971976; 22226667; 25662573

19 Jun 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: FCN3 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal

19 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: FCN3 were set to Immunodeficiency due to ficolin 3 deficiency, 613860; Ficolin3 deficiency

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to FCN3. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to FCN3. Panel: Primary immunodeficiency disorders Phenotypes for gene FCN3 were set to Immunodeficiency due to ficolin 3 deficiency, Ficolin3 deficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene FCN3 were set to Immunodeficiency due to ficolin 3 deficiency

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

FCN3 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

FCN3 was created by Louise Daugherty