FCN2

ficolin 2, the group of Fibrinogen C domain containing|Complement system activation components

Basic information

Region (hg38): 9:134880809-134887523

Links

ENSG00000160339 ∙ NCBI:2220 ∙ OMIM:601624 ∙ HGNC:3624 ∙ Uniprot:Q15485 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FCN2 gene.

• Inborn genetic diseases (15 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			15	1	3	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	1	4

Variants in FCN2

This is a list of pathogenic ClinVar variants found in the FCN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-134880832-A-T			Benign (Jul 21, 2017)
9-134880844-G-A		not specified	Uncertain significance (Jul 05, 2023)
9-134880854-C-T			Benign (Jul 21, 2017)
9-134882543-C-G		not specified	Uncertain significance (Jun 09, 2022)
9-134882550-G-T		not specified	Uncertain significance (Oct 06, 2021)
9-134883307-C-T		not specified	Uncertain significance (Jan 23, 2024)
9-134883308-G-A		not specified	Uncertain significance (Feb 21, 2024)
9-134883353-A-G		not specified	Uncertain significance (Sep 19, 2022)
9-134884761-C-T		not specified	Uncertain significance (Jul 06, 2021)
9-134885242-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-134885244-C-T			Benign (Jul 21, 2017)
9-134885254-A-G			Benign (Jul 01, 2022)
9-134885274-C-T			Likely benign (Jul 01, 2023)
9-134885320-C-A		not specified	Uncertain significance (Nov 08, 2022)
9-134885343-G-C		not specified	Uncertain significance (Jul 14, 2023)
9-134885350-A-G		not specified	Uncertain significance (Jan 23, 2023)
9-134885352-G-A		not specified	Uncertain significance (Oct 24, 2023)
9-134885372-T-C			Benign (Jul 21, 2017)
9-134885807-C-T		not specified	Uncertain significance (May 15, 2023)
9-134885812-C-A		not specified	Uncertain significance (Feb 14, 2024)
9-134885816-G-A		not specified	Uncertain significance (Dec 28, 2022)
9-134885837-G-A		not specified	Uncertain significance (Jul 19, 2022)
9-134885853-A-T		not specified	Uncertain significance (Sep 22, 2022)
9-134885882-G-T		not specified	Uncertain significance (Apr 13, 2022)
9-134886510-G-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCN2	protein_coding	protein_coding	ENST00000291744	8	7271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.56e-11	0.0485	125493	1	254	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.361	204	190	1.07	0.0000113	2009
Missense in Polyphen		64	57.809	1.1071		694
Synonymous	-0.767	90	81.2	1.11	0.00000523	633
Loss of Function	-0.0309	16	15.9	1.01	9.52e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00111
Ashkenazi Jewish	0.00	0.00
East Asian	0.00740	0.00737
Finnish	0.00	0.00
European (Non-Finnish)	0.000561	0.000545
Middle Eastern	0.00740	0.00737
South Asian	0.000863	0.000850
Other	0.000988	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in innate immunity through activation of the lectin complement pathway. Calcium-dependent and GlcNAc- binding lectin. Enhances phagocytosis of S.typhimurium by neutrophils, suggesting an opsonic effect via the collagen region. {ECO:0000269|PubMed:10679061, ECO:0000269|PubMed:17215869}.
• Pathway: Human Complement System;Innate Immune System;Immune System;Initial triggering of complement;Ficolins bind to repetitive carbohydrate structures on the target cell surface;Lectin pathway of complement activation;Creation of C4 and C2 activators;Complement cascade (Consensus)

Recessive Scores

• pRec: 0.0963

Intolerance Scores

• loftool: 0.573
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.3

Haploinsufficiency Scores

• pHI: 0.0980
• hipred: N
• hipred_score: 0.133
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Fcnb
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: complement activation, lectin pathway;proteolysis;complement activation;opsonization;recognition of apoptotic cell;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: extracellular region;collagen trimer;extracellular exosome;blood microparticle
• Molecular function: antigen binding;serine-type endopeptidase activity;protein binding;proteoglycan binding;metal ion binding;calcium-dependent protein binding;mannan binding