C1RL

complement C1r subcomponent like, the group of Sushi domain containing

Basic information

Region (hg38): 12:7089586-7109238

Links

ENSG00000139178 ∙ NCBI:51279 ∙ OMIM:608974 ∙ HGNC:21265 ∙ Uniprot:Q9NZP8 ∙ 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 C1RL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1RL 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						0
missense			30	6		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	6	0

Variants in C1RL

This is a list of pathogenic ClinVar variants found in the C1RL region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7089608-C-T			Benign (Jan 29, 2020)
12-7089616-T-C		Ehlers-Danlos syndrome, periodontal type 1	Likely benign (Jun 24, 2022)
12-7089671-G-A		C1R-related disorder	Likely benign (Sep 17, 2019)
12-7089707-T-C			Uncertain significance (Oct 01, 2018)
12-7089708-G-T		Ehlers-Danlos syndrome, periodontal type 1	Uncertain significance (Jul 23, 2021)
12-7089713-G-A		Ehlers-Danlos syndrome, periodontal type 1	Uncertain significance (Mar 30, 2021)
12-7089747-A-G			Uncertain significance (Jan 18, 2017)
12-7090054-A-G		Ehlers-Danlos syndrome, periodontal type 1	Uncertain significance (Apr 21, 2023)
12-7090061-G-A		Ehlers-Danlos syndrome, periodontal type 1	Uncertain significance (Jul 27, 2021)
12-7090085-T-A		not specified	Uncertain significance (Nov 03, 2023)
12-7090114-G-A		C1R-related disorder	Likely benign (Feb 21, 2023)
12-7090144-C-G		Ehlers-Danlos syndrome, periodontal type 1 • Vascular dementia	Conflicting classifications of pathogenicity (Aug 01, 2021)
12-7090146-T-C		C1R-related disorder	Uncertain significance (Feb 27, 2023)
12-7090203-C-A		Ehlers-Danlos syndrome, periodontal type 1	Uncertain significance (Jan 28, 2022)
12-7090215-A-G		Ehlers-Danlos syndrome	Likely pathogenic (Apr 25, 2020)
12-7090257-A-G		C1R-related disorder	Likely benign (Jul 07, 2021)
12-7090267-G-T			Benign (May 10, 2021)
12-7090354-A-G			Benign (May 10, 2021)
12-7090357-A-G			Benign (May 10, 2021)
12-7090444-C-T			Benign (May 10, 2021)
12-7091446-C-T		Ehlers-Danlos syndrome, periodontal type 1	Likely benign (Jul 25, 2022)
12-7091480-G-A		Ehlers-Danlos syndrome, periodontal type 1	Uncertain significance (May 31, 2022)
12-7091508-C-T			Likely benign (Jul 01, 2024)
12-7091533-GA-AT		Ehlers-Danlos syndrome, periodontal type 1 • Ehlers-Danlos syndrome, periodontal type 2	Pathogenic (Aug 23, 2016)
12-7091595-T-A			Uncertain significance (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1RL	protein_coding	protein_coding	ENST00000266542	6	19687

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.46e-8	0.553	125701	0	45	125746	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.902	243	286	0.850	0.0000158	3169
Missense in Polyphen		65	67.41	0.96424		756
Synonymous	0.281	120	124	0.968	0.00000791	967
Loss of Function	1.05	14	18.9	0.739	8.10e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000809	0.0000791
Middle Eastern	0.000382	0.000381
South Asian	0.000706	0.000686
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the proteolytic cleavage of HP/haptoglobin in the endoplasmic reticulum. {ECO:0000269|PubMed:15358180, ECO:0000269|PubMed:15385675, ECO:0000269|PubMed:15527420}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.262
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• pHI: 0.0859
• hipred: N
• hipred_score: 0.112
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1rl
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Biological process: complement activation, classical pathway;zymogen activation;innate immune response
• Cellular component: extracellular space;extracellular exosome
• Molecular function: serine-type endopeptidase activity