CR1

complement C3b/C4b receptor 1 (Knops blood group), the group of CD molecules|Sushi domain containing|Complement system regulators and receptors|Blood group antigens

Basic information

Region (hg38): 1:207496147-207641765

Links

ENSG00000203710

∙ NCBI:1378 ∙ OMIM:120620 ∙ HGNC:2334 ∙ Uniprot:P17927 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Knops system	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	11724985

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CR1 gene.

not_specified (210 variants)
not_provided (24 variants)
KNOPS_BLOOD_GROUP_SYSTEM (6 variants)
CR1-related_disorder (5 variants)
Malaria,_susceptibility_to (4 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Anxiety (1 variants)
Hypothyroidism (1 variants)
Polyarticular_arthritis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000651.6. 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	9 clinvar	1 clinvar	11
missense			199 clinvar	20 clinvar	4 clinvar	223
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	201	29	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CR1	protein_coding	protein_coding	ENST00000367049	47	144501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.65e-35	0.0105	124394	2	250	124646	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.474	927	887	1.04	0.0000476	16327
Missense in Polyphen		249	257.19	0.96815		4937
Synonymous	-1.34	358	327	1.09	0.0000186	4762
Loss of Function	1.82	64	81.8	0.783	0.00000478	1455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00144	0.00131
Ashkenazi Jewish	0.00	0.00
East Asian	0.00201	0.00200
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.00113	0.00110
Middle Eastern	0.00201	0.00200
South Asian	0.00189	0.00186
Other	0.000674	0.000661

dbNSFP

Source: dbNSFP

Function: FUNCTION: Mediates cellular binding of particles and immune complexes that have activated complement.;
Pathway: Complement and coagulation cascades - Homo sapiens (human);Legionellosis - Homo sapiens (human);Malaria - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Primary Focal Segmental Glomerulosclerosis FSGS;Human Complement System;Dengue-2 Interactions with Complement and Coagulation Cascades;RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);Complement and Coagulation Cascades;Neutrophil degranulation;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Innate Immune System;Immune System;Regulation of Complement cascade;Complement cascade;RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);Transcriptional regulation by RUNX1 (Consensus)

Haploinsufficiency Scores

pHI: 0.0878
hipred: N
hipred_score: 0.389
ghis: 0.413

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.764

Gene Damage Prediction

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

Gene ontology

Biological process: complement receptor mediated signaling pathway;complement activation, classical pathway;regulation of complement activation;neutrophil degranulation;innate immune response;regulation of regulatory T cell differentiation;negative regulation of complement activation, alternative pathway;negative regulation of complement activation, classical pathway;viral entry into host cell;negative regulation of serine-type endopeptidase activity;positive regulation of serine-type endopeptidase activity
Cellular component: plasma membrane;integral component of plasma membrane;cell surface;secretory granule membrane;extracellular exosome;ficolin-1-rich granule membrane
Molecular function: virus receptor activity;complement component C3b binding;complement component C4b binding;complement component C4b receptor activity;complement component C3b receptor activity