FCN2

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

Basic information

Region (hg38): 9:134880810-134887523

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.

not_specified (46 variants)
not_provided (7 variants)
Susceptibility_to_severe_COVID-19 (1 variants)
FCN2-related_disorder (1 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. These statistics are base on transcript: NM_000004108.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			47 clinvar	1 clinvar	3 clinvar	51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	0	1	47	2	4

Loading clinvar variants...

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