C1S
protein-codingcomplement C1s, the group of Sushi domain containing|Complement system activation components
Gene summary
This gene encodes a serine protease, which is a major constituent of the human complement subcomponent C1. C1s associates with two other complement components C1r and C1q in order to yield the first component of the serum complement system. Defects in this gene are the cause of selective C1s deficiency. [provided by RefSeq, Mar 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~82.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0014954
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0013419
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014954
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0014954
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013419
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007527
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0014954
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Dental; Dermatologic; Musculoskeletal; Oncologic; Renal
Intervention: Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Oncologic
Rationale: Ehlers-Danlos syndrome, periodontal type has been described as inolving risk of arterial and gastrointestinal rupture as well as recurrent infections, and awareness may allow prompt diagnosis and management; Individuals with Ehlers-Danlos syndrome, periodontal have been described with Wilms tumor (as well as other types of neoplasms), and awareness may allow early detection and treatment; Individuals with Complement component C1s deficiency may suffer from conditions such as severe infections, for which prophylaxis and/or early and aggressive treatment of infection may be beneficial; Immunosuppression may be beneficial for autoimmune phenomena (such as lupus nephritis)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to C1S variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001734.5. 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 | 8 | 143 | 151 | |||
| missense | 1 | 364 | 17 | 382 | ||
| nonsense | 10 | 1 | 11 | |||
| start loss | 1 | 1 | ||||
| frameshift | 15 | 5 | 6 | 26 | ||
| splice donor/acceptor (+/-2bp) | 6 | 6 | 12 | |||
| Total | 26 | 13 | 384 | 160 | 0 | 583 |
Highest pathogenic variant AF is 0.000031503525
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001725.1 | 11 | MANE Select | |
| Ensembl | ENSP00000354057.5 | 11 | MANE Select | |
| RefSeq | NP_001333779.1 | 8 | Standard | |
| RefSeq | NP_958850.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Complement and coagulation cascades - Homo sapiens (human)
- Pertussis - Homo sapiens (human)
- Systemic lupus erythematosus - Homo sapiens (human)
- Staphylococcus aureus infection - Homo sapiens (human)
- Human Complement System
Biological Process
- proteolysis
- complement activation
- complement activation, classical pathway
- regulation of complement activation
- innate immune response
Molecular Function
- serine-type endopeptidase activity
- calcium ion binding
- protein binding
- identical protein binding
Cellular Component
- extracellular region
- extracellular space
- blood microparticle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000406697
- Coding exons
- 11
- Length
- 81986
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 125748
- p
- 0.000103
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.559 | 342 | 372 | 0.918 | 0.0000206 | 4527 |
| Missense (PolyPhen) | 100 | 136.19 | 0.73429 | 1735 | ||
| Synonymous | -0.392 | 144 | 138 | 1.04 | 0.00000779 | 1318 |
| Loss of Function | 3.28 | 11 | 30.5 | 0.360 | 0.00000164 | 381 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: C1s B chain is a serine protease that combines with C1q and C1r to form C1, the first component of the classical pathway of the complement system. C1r activates C1s so that it can, in turn, activate C2 and C4.;
- Disease
- DISEASE: Complement component C1s deficiency (C1SD) [MIM:613783]: A rare defect resulting in C1 deficiency and impaired activation of the complement classical pathway. C1 deficiency generally leads to severe immune complex disease with features of systemic lupus erythematosus and glomerulonephritis. {ECO:0000269|PubMed:11390518}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ehlers-Danlos syndrome, periodontal type, 2 (EDSPD2) [MIM:617174]: A form of Ehlers-Danlos syndrome, a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDSPD2 is characterized by the association of typical features of Ehlers-Danlos syndrome with gingival recession and severe early- onset periodontal disease, leading to premature loss of permanent teeth. EDSPD2 transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27745832}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.443
Intolerance Scores
- LoFtool
- 0.189
- RVIS EVS
- -0.04
- RVIS percentile EVS
- 50.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.935
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |