CFP

complement factor properdin, the group of Complement system activation components

Basic information

Region (hg38): X:47623171-47630305

Previous symbols: [ "PFC" ]

Links

ENSG00000126759 ∙ NCBI:5199 ∙ OMIM:300383 ∙ HGNC:8864 ∙ Uniprot:P27918 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• properdin deficiency, X-linked (Supportive), mode of inheritance: XL
• properdin deficiency, X-linked (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Properdin deficiency, X-linked	XL	Allergy/Immunology/Infectious	Individuals are especially susceptible to Neisseria infections, warranting infectious prophylaxis and early and aggressive treatment of infections	Allergy/Immunology/Infectious	8530058; 8871668; 10909851; 22229731

ClinVar

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

• not provided (116 variants)
• Inborn genetic diseases (6 variants)
• Properdin deficiency, X-linked (4 variants)
• not specified (2 variants)
• Properdin deficiency, type II (1 variants)
• CFP-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFP 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			2	31	4	37
missense	1		55	2	7	65
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			1	1	1	3
non coding			1	10	1	12
Total	1	1	60	43	12

Highest pathogenic variant AF is 0.00000921

Variants in CFP

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

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

Position	Type	Phenotype	Significance	ClinVar
X-47624273-T-A		CFP-related disorder	Benign (Jul 11, 2019)
X-47624278-G-C			Likely benign (Jun 27, 2022)
X-47624311-C-T			Likely benign (Jan 08, 2024)
X-47624316-G-A			Uncertain significance (Dec 07, 2023)
X-47624325-G-A		Inborn genetic diseases	Uncertain significance (Jan 17, 2024)
X-47624325-G-C		CFP-related disorder	Uncertain significance (Jul 10, 2023)
X-47624337-C-T			Uncertain significance (Nov 23, 2021)
X-47624342-A-G			Uncertain significance (Feb 04, 2023)
X-47624353-C-A			Benign (Nov 13, 2023)
X-47624353-C-T			Likely benign (Aug 24, 2022)
X-47624356-T-C			Likely benign (Apr 07, 2022)
X-47624361-G-A			Likely benign (Jan 08, 2023)
X-47624365-C-T			Uncertain significance (Aug 22, 2021)
X-47624372-C-T			Uncertain significance (Jul 07, 2023)
X-47624376-G-T			Uncertain significance (Jun 13, 2022)
X-47624384-C-G			Uncertain significance (Dec 21, 2021)
X-47624384-C-T			Uncertain significance (Dec 07, 2022)
X-47624394-A-C		Inborn genetic diseases	Uncertain significance (Aug 22, 2023)
X-47624401-G-A		not specified	Benign (Feb 01, 2024)
X-47624449-T-TTAGGGGTGGGGAGGAACGGAAGGGAGAATCTCAGGGAAGGCAAGAATGCATTCAATTCTTATTGAGTGCCTCAGGCCC			Uncertain significance (Oct 11, 2023)
X-47624450-TA-T			Likely benign (Aug 23, 2023)
X-47624454-G-A			Likely benign (Sep 01, 2023)
X-47626039-A-G			Likely benign (Feb 11, 2022)
X-47626045-C-T			Likely benign (Oct 25, 2023)
X-47626057-C-T			Uncertain significance (Feb 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFP	protein_coding	protein_coding	ENST00000247153	9	6093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.688	0.312	125592	3	1	125596	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	115	202	0.571	0.0000173	2952
Missense in Polyphen		36	84.21	0.4275		1144
Synonymous	0.988	68	79.2	0.859	0.00000666	931
Loss of Function	3.47	4	21.3	0.188	0.00000172	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000495	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: A positive regulator of the alternate pathway of complement. It binds to and stabilizes the C3- and C5-convertase enzyme complexes. {ECO:0000269|PubMed:20382442}.
• Disease: DISEASE: Properdin deficiency (PFD) [MIM:312060]: Results in higher susceptibility to bacterial infections; especially to meningococcal infections. Three phenotypes have been reported: complete deficiency (type I), incomplete deficiency (type II), and dysfunction of properdin (type III). {ECO:0000269|PubMed:10909851, ECO:0000269|PubMed:8871668, ECO:0000269|PubMed:9710744}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Herpes simplex infection - Homo sapiens (human);Human Complement System;Complement Activation;Neutrophil degranulation;alternative complement pathway;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.268

Intolerance Scores

• loftool: 0.330
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.573
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cfp
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype

Gene ontology

• Biological process: proteolysis;immune response;complement activation;complement activation, alternative pathway;regulation of complement activation;defense response to bacterium;neutrophil degranulation
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;specific granule lumen;collagen-containing extracellular matrix;tertiary granule lumen
• Molecular function: serine-type endopeptidase activity;protein binding