CR1 (Complement receptor type 1) variants and mutations
CR1 (also known as Complement receptor type 1) is a human protein-coding gene encoding a complement receptor type 1 protein. It binds C3b and C4b, promotes clearance of complement-coated immune complexes, and helps restrain complement activation on cell surfaces. Copy-number and sequence variation can influence complement biology and has been associated with diseases including Alzheimer disease and malaria-related phenotypes. This analysis covers 66 CR1 variants and mutations. Of these, 94% have computational variant effect predictions. Disease context includes Alzheimer disease, dementia, and late-onset Alzheimers disease. Example CR1 variants include G2V, A3S, and A3A.
Variant analysis overview
- Gene: CR1
- Protein: Complement receptor type 1
- UniProt accession: P17927
- Organism: Homo sapiens
- Variants analyzed: 66
- Variant scope: all variants
- Completed: 2026-08-21
Variant and mutation evidence
- Variant composition: 11 unspecified-consequence records; 38 missense variants; 13 synonymous variants; 1 frameshift variants; 3 substitution
- Prediction scores: 62 variants have prediction scores (94% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Alzheimer disease, dementia, late-onset Alzheimers disease, neurodegenerative disease, Splenomegaly, chronic intestinal vascular insufficiency, hypothyroidism, polyarticular arthritis, Anxiety, systemic lupus erythematosus, neoplasm, hepatocellular carcinoma.
Protein structure and variant hotspots
- Protein features: 1 transmembrane segments; 30 domains; 21 post-translational modification sites.
- Structural context: 10 variants have structural context.
- PTM context: 1 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable CR1 variants
Examples include G2V, A3S, A3A, S4F, S4S, S5P, S5A, S5C. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- G2V (p.Gly2Val), rs1179458153, gnomAD 1-207496272-G-T, REVEL 0.04, MetaLR 0.03
- A3S (p.Ala3Ser), rs1438089128, gnomAD 1-207496274-G-T, REVEL 0.04, MetaLR 0.04
- A3A (p.Ala3Ala), gnomAD 1-207496276-C-T, CADD 8.54
- S4F (p.Ser4Phe), gnomAD 1-207496278-C-T, REVEL 0.02, MetaLR 0.04
- S4S (p.Ser4Ser), gnomAD 1-207496279-T-C, CADD 7.62
- S5P (p.Ser5Pro), gnomAD 1-207496280-T-C, REVEL 0.13, MetaLR 0.08
- S5A (p.Ser5Ala), rs1270698778, gnomAD 1-207496280-T-G, REVEL 0.03, MetaLR 0.05
- S5C (p.Ser5Cys), gnomAD 1-207496281-C-G, REVEL 0.11, MetaLR 0.09
- P6L (p.Pro6Leu), gnomAD 1-207496284-C-T, REVEL 0.03, MetaLR 0.05
- P6P (p.Pro6Pro), gnomAD 1-207496285-A-G, CADD 6.09
- R7G (p.Arg7Gly), rs1038479607, gnomAD 1-207496286-A-G, REVEL 0.20, MetaLR 0.08
- R7K (p.Arg7Lys), gnomAD 1-207496287-G-A, REVEL 0.14, MetaLR 0.08
- P9Q (p.Pro9Gln), gnomAD 1-207496293-C-A, REVEL 0.06, MetaLR 0.04
- P9P (p.Pro9Pro), gnomAD 1-207496294-G-A, CADD 4.60
- P11T (p.Pro11Thr), rs781322624, gnomAD 1-207496298-C-A, REVEL 0.06, MetaLR 0.07
- P11A (p.Pro11Ala), rs781322624, gnomAD 1-207496298-C-G, REVEL 0.05, MetaLR 0.06
- P11P (p.Pro11Pro), gnomAD 1-207496300-T-A, CADD 6.93
- V12I (p.Val12Ile), rs372551774, gnomAD 1-207496301-G-A, REVEL 0.03, MetaLR 0.04
- V12V (p.Val12Val), rs996388913, gnomAD 1-207496303-C-T, CADD 3.34
- G13R (p.Gly13Arg), gnomAD 1-207496304-G-A, REVEL 0.02, MetaLR 0.03
- G13W (p.Gly13Trp), gnomAD 1-207496304-G-T, REVEL 0.02, MetaLR 0.04
- P14S (p.Pro14Ser), gnomAD 1-207496307-C-T, REVEL 0.09, MetaLR 0.08
- P14L (p.Pro14Leu), gnomAD 1-207496308-C-T, REVEL 0.04, MetaLR 0.03
- P14Q (p.Pro14Gln), rs769828093, gnomAD 1-207496308-C-A, REVEL 0.08, MetaLR 0.09
- P14P (p.Pro14Pro), rs1659077890, gnomAD 1-207496309-G-A, CADD 7.55
- P15S (p.Pro15Ser), rs1402904259, gnomAD 1-207496310-C-T, REVEL 0.01, MetaLR 0.04
- P15L (p.Pro15Leu), rs775590306, gnomAD 1-207496311-C-T, REVEL 0.01, MetaLR 0.03
- P15R (p.Pro15Arg), gnomAD 1-207496311-C-G, REVEL 0.01, MetaLR 0.04
- P15P (p.Pro15Pro), gnomAD 1-207496312-G-T, CADD 5.64
- A16T (p.Ala16Thr), rs369804986, gnomAD 1-207496313-G-A, REVEL 0.01, MetaLR 0.04
- A16G (p.Ala16Gly), rs774774612, gnomAD 1-207496314-C-G, REVEL 0.02, MetaLR 0.03
- A16E (p.Ala16Glu), rs774774612, gnomAD 1-207496314-C-A, REVEL 0.01, MetaLR 0.03
- A16A (p.Ala16Ala), rs373914260, gnomAD 1-207496315-G-T, CADD 5.74
- P17S (p.Pro17Ser), rs772948093, gnomAD 1-207496316-C-T, REVEL 0.03, MetaLR 0.03
- P17R (p.Pro17Arg), rs566717082, gnomAD 1-207496317-C-G, REVEL 0.02, MetaLR 0.03
- P17P (p.Pro17Pro), rs765951976, gnomAD 1-207496318-C-T, CADD 5.24
- G18S (p.Gly18Ser), rs1318306169, gnomAD 1-207496319-G-A, REVEL 0.02, MetaLR 0.03
- G18C (p.Gly18Cys), gnomAD 1-207496319-G-T, REVEL 0.03, MetaLR 0.03
- G18R (p.Gly18Arg), gnomAD 1-207496319-G-C, REVEL 0.02, MetaLR 0.02
- G18A (p.Gly18Ala), rs1197723622, gnomAD 1-207496320-G-C, REVEL 0.00, MetaLR 0.02
- G18V (p.Gly18Val), rs1197723622, gnomAD 1-207496320-G-T, REVEL 0.01, MetaLR 0.03
- L19F (p.Leu19Phe), rs575513177, gnomAD 1-207496322-C-T, REVEL 0.11, MetaLR 0.06
- L19H (p.Leu19His), rs1255951917, gnomAD 1-207496323-T-A, REVEL 0.17, MetaLR 0.07
- L19L (p.Leu19Leu), rs753333659, gnomAD 1-207496324-C-A, CADD 1.48
- P20A (p.Pro20Ala), gnomAD 1-207496325-C-G, REVEL 0.03, MetaLR 0.03
- P20S (p.Pro20Ser), gnomAD 1-207496325-C-T, REVEL 0.01, MetaLR 0.03
- P20L (p.Pro20Leu), rs199732885, gnomAD 1-207496326-C-T, REVEL 0.03, MetaLR 0.03
- P20P (p.Pro20Pro), rs765154374, gnomAD 1-207496327-C-T, CADD 7.28
- F21L (p.Phe21Leu), rs1423387453, gnomAD 1-207496330-C-G, REVEL 0.02, MetaLR 0.03
- C22R (p.Cys22Arg), rs1186041714, gnomAD 1-207496331-T-C, REVEL 0.03, MetaLR 0.04
- C22C (p.Cys22Cys), gnomAD 1-207496333-C-T, CADD 11.00
- G24R (p.Gly24Arg), rs1659080438, gnomAD 1-207496336-C-CA, CADD 15.80
- S130F (p.Ser130Phe), rs779758291, []
- Q221P (p.Gln221Pro), rs905671575, []
- P240L (p.Pro240Leu), rs781450002, []
- H1208R (p.His1208Arg), rs2274567, UniProt VAR 013819, AlphaMissense 0.11, MetaLR 0.00
- T1408I (p.Thr1408Ile), UniProt VAR 013820
- T1408M (p.Thr1408Met), rs3737002, UniProt VAR 020263, AlphaMissense 0.11, MetaLR 0.00
- N1540S (p.Asn1540Ser), rs17259045, UniProt VAR 055685, AlphaMissense 0.06, MetaLR 0.00, Benign, CR1-related disorder
- K1590E (p.Lys1590Glu), rs17047660, UniProt VAR 013821, AlphaMissense 0.17, MetaLR 0.00, Benign, CR1-related disorder
- R1601G (p.Arg1601Gly), rs17047661, UniProt VAR 013822, AlphaMissense 0.22, MetaLR 0.00, Benign, CR1-related disorder
- S1610T (p.Ser1610Thr), rs4844609, UniProt VAR 013823, AlphaMissense 0.07, MetaLR 0.20, Benign, in Sl(3) antigen
- I1615V (p.Ile1615Val), rs6691117, UniProt VAR 013824, AlphaMissense 0.08, MetaLR 0.00, Benign, not provided
- P1827R (p.Pro1827Arg), rs3811381, UniProt VAR 013825, AlphaMissense 0.09, MetaLR 0.04, Benign, CR1-related disorder
- H1850D (p.His1850Asp), UniProt VAR 013826
- T1969A (p.Thr1969Ala), rs2296160, UniProt VAR 055686, AlphaMissense 0.08, MetaLR 0.00
Public CR1 analysis runs
- CR1 analysis run — CR1 (66 variants) — completed 2026-08-21