C4BPA

complement component 4 binding protein alpha, the group of Sushi domain containing|Complement system regulators and receptors

Basic information

Region (hg38): 1:207104232-207144972

Previous symbols: [ "C4BP" ]

Links

ENSG00000123838 ∙ NCBI:722 ∙ OMIM:120830 ∙ HGNC:1325 ∙ Uniprot:P04003 ∙ 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 C4BPA gene.

• not provided (21 variants)
• Inborn genetic diseases (21 variants)
• not specified (2 variants)
• C4BPA-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4BPA 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					3	3
missense			21	1	8	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					10	10
Total	0	0	21	1	21

Variants in C4BPA

This is a list of pathogenic ClinVar variants found in the C4BPA region.

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

Position	Type	Phenotype	Significance	ClinVar
1-207113035-C-G			Benign (Dec 31, 2019)
1-207113036-C-A			Benign (Jun 09, 2021)
1-207113045-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-207113053-G-A		not specified	Likely benign (Jul 13, 2022)
1-207113054-C-T		not specified	Uncertain significance (Jun 06, 2022)
1-207113064-A-G			Benign (Dec 31, 2019)
1-207113083-T-C		not specified	Uncertain significance (Nov 30, 2022)
1-207113095-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-207113111-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-207113122-C-G			Benign (Dec 31, 2019)
1-207113412-T-C			Benign (Jun 18, 2021)
1-207113842-C-T			Benign (Jun 18, 2021)
1-207114109-G-A		not specified	Likely benign (Mar 01, 2024)
1-207114136-C-T			Benign (Dec 31, 2019)
1-207114184-C-T		not specified	Uncertain significance (Mar 30, 2022)
1-207114485-CT-C			Benign (Jun 18, 2021)
1-207115437-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-207115552-T-C			Benign (Nov 10, 2018)
1-207124139-G-C			Benign (Nov 10, 2018)
1-207124246-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-207124265-G-T		not specified	Uncertain significance (Oct 13, 2023)
1-207124277-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-207124300-T-A		C4BPA-related disorder	Uncertain significance (May 16, 2023)
1-207124331-T-C			Benign (Dec 31, 2019)
1-207124335-T-C		not specified	Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4BPA	protein_coding	protein_coding	ENST00000367070	11	40711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.457	0.543	125701	0	12	125713	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	244	325	0.750	0.0000168	3888
Missense in Polyphen		39	105.05	0.37126		1323
Synonymous	-0.0251	118	118	1.00	0.00000642	1121
Loss of Function	3.80	6	27.6	0.218	0.00000126	365

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)	0.000100	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls the classical pathway of complement activation. It binds as a cofactor to C3b/C4b inactivator (C3bINA), which then hydrolyzes the complement fragment C4b. It also accelerates the degradation of the C4bC2a complex (C3 convertase) by dissociating the complement fragment C2a. Alpha chain binds C4b. It interacts also with anticoagulant protein S and with serum amyloid P component.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Pertussis - Homo sapiens (human);Human Complement System;Innate Immune System;Immune System;Regulation of Complement cascade;Complement cascade;CD40/CD40L signaling (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.620
• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.75

Haploinsufficiency Scores

• pHI: 0.0647
• hipred: N
• hipred_score: 0.233

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0781

Gene Damage Prediction

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

Gene ontology

• Biological process: complement activation, classical pathway;regulation of complement activation;innate immune response;positive regulation of protein catabolic process;negative regulation of complement activation, classical pathway;regulation of opsonization
• Cellular component: extracellular region;extracellular space;plasma membrane;other organism cell;blood microparticle
• Molecular function: RNA binding;protein binding