CR1L

protein-coding

complement C3b/C4b receptor 1 like, the group of Sushi domain containing

Gene summary

Acts upstream of or within regulation of complement activation and regulation of complement-dependent cytotoxicity. Part of signaling receptor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_175710.2

Inheritance

—

ClinVar variants

U:100B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.23

Max pathogenic AF

—

Genomic locus

chr1:207,645,113-207,738,416

External References & Databases

Ensembl (ENSG00000197721)

Transcript & Mutation Effects

hg38 • Region Span ~93.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CR1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_175710.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			99 clinvar	10 clinvar		109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	100	13	0	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_175710.2	RefSeq	NP_783641.1	12	MANE Select
ENST00000508064.7	Ensembl	ENSP00000421736.2	12	MANE Select
ENST00000294997.10	Ensembl	ENSP00000434864.1	9	Standard
ENST00001131197.1	Ensembl	ENSP00000801002.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region
cytoplasm
membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000508064
Coding exons: 12
Length: 93304
Individuals with no LoFs: 124475
Homozygous LoFs: 1
Heterozygous LoFs: 165
Defined: 124641
p: 0.000666

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.670	342	309	1.11	0.0000161	3706
Missense (PolyPhen)		102	97.67	1.0443		1218
Synonymous	-1.96	140	114	1.23	0.00000599	1099
Loss of Function	-1.14	36	29.3	1.23	0.00000177	329

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00061	0.00052	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0010	0.0010	notable
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.00057	0.00057	rare
South Asian	0.0019	0.0019	notable
Other	0.00083	0.00083	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.821
RVIS EVS: 3.87
RVIS percentile EVS: 99.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.544

Gene Damage Prediction

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