CD55

CD55 molecule (Cromer blood group), the group of CD molecules|Sushi domain containing|Complement system regulators and receptors|Blood group antigens

Basic information

Region (hg38): 1:207321519-207386804

Previous symbols: [ "DAF" ]

Links

ENSG00000196352 ∙ NCBI:1604 ∙ OMIM:125240 ∙ HGNC:2665 ∙ Uniprot:P08174 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• protein-losing enteropathy (Supportive), mode of inheritance: AR
• protein-losing enteropathy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Cromer system; Complement hyperactivation, angiopathic thrombosis, and protein-losing enteropathy	BG/AR	Hematologic	For Complement hyperactivation, angiopathic thrombosis, and protein-losing enteropathy, individuals may manifest with features denoted by the condition name, with signs and symptoms including abdominal pain/diarrhea, intestinal lymphangiectasia, hypoproteinemic edema, and malabsorption, as well as recurrent infections; with hypogammaglobulinemia, and angiopathic thromboembolism, and medical management (eg, with terminal complement inhibitor eculizumab) has been described as beneficial on laboratory and clinical parameters; The condition can include recurrent infections, and awareness may allow preventative measures and early and aggressive treatment of infections; Blood group, Cromer system, variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	7519480; 8837357; 9427725; 21214297; 28657829; 28657861

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD55 gene.

• not provided (7 variants)
• Cromer blood group system (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD55 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				43	4	47
missense			71	7	3	81
nonsense	5	2	1			8
start loss			1			1
frameshift	2		2			4
inframe indel			5			5
splice donor/acceptor (+/-2bp)		6	1			7
splice region			6	6	1	13
non coding			1	36	5	42
Total	7	8	82	86	12

Highest pathogenic variant AF is 0.0000197

Variants in CD55

This is a list of pathogenic ClinVar variants found in the CD55 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-207321766-A-AT			Uncertain significance (Oct 13, 2022)
1-207321769-A-G		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
1-207321771-C-G			Benign (Jan 19, 2024)
1-207321780-G-A			Likely benign (Jul 08, 2023)
1-207321782-C-A			Uncertain significance (Mar 12, 2022)
1-207321783-G-A			Likely benign (Apr 26, 2023)
1-207321786-C-T			Likely benign (Jul 28, 2023)
1-207321789-G-A			Likely benign (Dec 22, 2023)
1-207321792-C-T			Likely benign (Jan 15, 2023)
1-207321799-C-T			Likely benign (Apr 30, 2023)
1-207321803-C-T			Uncertain significance (Sep 01, 2021)
1-207321804-C-A			Likely benign (Nov 21, 2023)
1-207321806-TC-T		Protein-losing enteropathy	Pathogenic (Aug 11, 2017)
1-207321808-C-T			Uncertain significance (May 20, 2022)
1-207321823-C-T			Uncertain significance (Jul 20, 2022)
1-207321835-C-T			Likely benign (Sep 20, 2022)
1-207321863-G-A		Protein-losing enteropathy	Pathogenic (Jul 11, 2024)
1-207321870-G-A			Uncertain significance (Feb 18, 2022)
1-207321879-C-A			Likely benign (Jan 31, 2024)
1-207321879-C-T			Benign (Jan 15, 2024)
1-207321882-C-T			Likely benign (Aug 31, 2021)
1-207321883-G-A			Likely benign (Nov 29, 2022)
1-207321884-GC-G			Likely benign (Oct 16, 2022)
1-207322363-T-C			Likely benign (May 19, 2022)
1-207322376-C-T			Likely benign (Sep 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD55	protein_coding	protein_coding	ENST00000314754	11	39459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.68e-12	0.114	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.923	190	229	0.828	0.0000116	2805
Missense in Polyphen		58	86.8	0.66821		1024
Synonymous	0.770	78	87.1	0.895	0.00000451	894
Loss of Function	0.573	19	21.9	0.868	0.00000114	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000172	0.000163
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.000226	0.000220
Middle Eastern	0.000172	0.000163
South Asian	0.000196	0.000196
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein recognizes C4b and C3b fragments that condense with cell-surface hydroxyl or amino groups when nascent C4b and C3b are locally generated during C4 and c3 activation. Interaction of daf with cell-associated C4b and C3b polypeptides interferes with their ability to catalyze the conversion of C2 and factor B to enzymatically active C2a and Bb and thereby prevents the formation of C4b2a and C3bBb, the amplification convertases of the complement cascade (PubMed:7525274). Inhibits complement activation by destabilizing and preventing the formation of C3 and C5 convertases, which prevents complement damage (PubMed:28657829). {ECO:0000269|PubMed:7525274, ECO:0000305|PubMed:28657829}.; FUNCTION: (Microbial infection) Acts as a receptor for Human enterovirus 70 and D68 (Probable). {ECO:0000269|PubMed:8764022}.
• Disease: DISEASE: Complement hyperactivation, angiopathic thrombosis, and protein-losing enteropathy (CHAPLE) [MIM:226300]: An autosomal recessive disease characterized by abdominal pain and diarrhea, primary intestinal lymphangiectasia, edema due to hypoproteinemia, malabsorption, and less frequently, bowel inflammation, recurrent infections, and angiopathic thromboembolic disease. Patients' T lymphocytes show increased complement activation causing surface deposition of complement and the generation of soluble C5a. {ECO:0000269|PubMed:28657829, ECO:0000269|PubMed:28657861}. Note=The disease is caused by mutations affecting the gene represented in this entry. CHAPLE is caused by biallelic mutations in the CD55 gene.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Allograft Rejection;Human Complement System;Dengue-2 Interactions with Complement and Coagulation Cascades;Complement Activation;Complement and Coagulation Cascades;Signaling by GPCR;Neutrophil degranulation;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Class B/2 (Secretin family receptors);GPCR ligand binding;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Regulation of Complement cascade;COPI-mediated anterograde transport;Complement cascade;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.364

Intolerance Scores

• loftool: 0.997
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.273
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.823

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd55b
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;complement activation, classical pathway;positive regulation of cytosolic calcium ion concentration;regulation of complement activation;regulation of lipopolysaccharide-mediated signaling pathway;CD4-positive, alpha-beta T cell cytokine production;neutrophil degranulation;innate immune response;respiratory burst;negative regulation of complement activation;viral entry into host cell;positive regulation of CD4-positive, alpha-beta T cell activation;positive regulation of CD4-positive, alpha-beta T cell proliferation
• Cellular component: Golgi membrane;extracellular region;plasma membrane;cell surface;transport vesicle;secretory granule membrane;anchored component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;membrane raft;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: virus receptor activity;protein binding;lipid binding