CR1L

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

Basic information

Region (hg38): 1:207645113-207738416

Links

ENSG00000197721 ∙ NCBI:1379 ∙ OMIM:605886 ∙ HGNC:2335 ∙ Uniprot:Q2VPA4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CR1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CR1L 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				2		2
missense			35	5		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	7	0

Variants in CR1L

This is a list of pathogenic ClinVar variants found in the CR1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-207645238-C-T		not specified	Uncertain significance (Mar 05, 2024)
1-207645264-T-C		not specified	Uncertain significance (Apr 07, 2023)
1-207645284-T-A			Likely benign (Jul 01, 2022)
1-207645298-C-A		not specified	Uncertain significance (Jun 01, 2023)
1-207677404-C-T		not specified	Uncertain significance (Feb 03, 2022)
1-207677487-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-207677509-C-G		not specified	Uncertain significance (Nov 08, 2022)
1-207677533-A-G		not specified	Uncertain significance (Jun 22, 2023)
1-207678221-G-C		not specified	Uncertain significance (Mar 26, 2024)
1-207678237-T-C		not specified	Uncertain significance (Apr 24, 2023)
1-207678249-T-A		not specified	Uncertain significance (Sep 14, 2022)
1-207678255-A-G		not specified	Uncertain significance (Apr 27, 2024)
1-207683889-C-A		not specified	Uncertain significance (Oct 12, 2021)
1-207683892-C-T		not specified	Uncertain significance (Mar 15, 2024)
1-207694361-T-C		not specified	Uncertain significance (Nov 17, 2022)
1-207694382-G-A		not specified	Uncertain significance (Mar 21, 2023)
1-207694446-A-G		not specified	Likely benign (Mar 31, 2023)
1-207694474-G-T		not specified	Uncertain significance (Jan 04, 2024)
1-207694540-G-C		not specified	Uncertain significance (Feb 17, 2022)
1-207694664-C-G		not specified	Uncertain significance (Sep 01, 2021)
1-207694667-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-207694693-C-T			Likely benign (Jul 01, 2022)
1-207694716-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-207697539-G-A		not specified	Likely benign (Jul 09, 2021)
1-207697552-C-G		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CR1L	protein_coding	protein_coding	ENST00000508064	12	93304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.64e-27	0.0000143	124475	1	165	124641	0.000666

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.670	342	309	1.11	0.0000161	3706
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000738	0.000738
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.00101	0.00100
Finnish	0.0000494	0.0000464
European (Non-Finnish)	0.000569	0.000566
Middle Eastern	0.00101	0.00100
South Asian	0.00190	0.00186
Other	0.000828	0.000826

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.821
• rvis_EVS: 3.87
• rvis_percentile_EVS: 99.65

Haploinsufficiency Scores

• pHI: 0.0696
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cr1l
• Phenotype: renal/urinary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Cellular component: extracellular region;cytoplasm;membrane;receptor complex