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): 1:207496146-207641765

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.

• Inborn genetic diseases (54 variants)
• not provided (18 variants)
• KNOPS BLOOD GROUP SYSTEM (2 variants)
• Hypothyroidism;Polyarticular arthritis;Anxiety (1 variants)
• Malaria, susceptibility to;KNOPS BLOOD GROUP SYSTEM (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.

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			1	5		6
missense			53	5	1	59
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				1		1
Total	0	0	55	11	1

Variants in CR1

This is a list of pathogenic ClinVar variants found in the CR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-207505930-C-T		not specified	Uncertain significance (Oct 22, 2021)
1-207506725-C-T			Benign (Dec 01, 2023)
1-207506757-G-T			Likely benign (Mar 01, 2024)
1-207506765-T-C		not specified	Uncertain significance (Jan 10, 2022)
1-207511640-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-207523652-T-G		not specified	Uncertain significance (Apr 04, 2023)
1-207523688-T-G		not specified	Uncertain significance (Jul 29, 2023)
1-207523721-G-A		not specified	Likely benign (Jan 08, 2024)
1-207523763-T-C		not specified	Uncertain significance (Aug 26, 2022)
1-207523911-A-C		not specified	Uncertain significance (Dec 04, 2023)
1-207523925-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-207523927-T-G			Likely benign (Mar 01, 2024)
1-207523933-T-C			Uncertain significance (Dec 01, 2016)
1-207523938-T-G		not specified	Uncertain significance (Feb 07, 2023)
1-207523952-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-207523953-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-207523972-G-A			Likely benign (Jul 01, 2023)
1-207526761-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-207526788-C-T		not specified	Conflicting classifications of pathogenicity (Jan 01, 2023)
1-207526856-C-T			Likely benign (Jun 01, 2023)
1-207526915-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-207526921-C-G		not specified	Likely benign (Sep 16, 2021)
1-207527080-A-T		not specified	Uncertain significance (Feb 03, 2022)
1-207534292-A-C		not specified	Likely benign (Aug 17, 2021)
1-207542212-C-T		not specified	Uncertain significance (Oct 27, 2022)

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