C1S

protein-coding

complement 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

NM_001734.5

Inheritance

AD, AR

ClinVar variants

P:39U:384B:160

Top phenotype

Ehlers-Danlos syndrome, periodontal type 2; Complement component C1s deficiency

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr12:6,988,259-7,071,032

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~82.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Ehlers-Danlos syndrome, periodontal type 2LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014954

Submitter: Ambry Genetics

complement component C1s deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013419

Submitter: Ambry Genetics

Ehlers-Danlos syndrome, periodontal type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014954

Submitter: Genomics England PanelApp

Ehlers-Danlos syndrome, periodontal type 2LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014954

Submitter: G2P

complement component C1s deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013419

Submitter: Labcorp Genetics (formerly Invitae)

Ehlers-Danlos syndrome, periodontitis typeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007527

Submitter: Orphanet

Ehlers-Danlos syndrome, periodontal type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014954

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Ehlers-Danlos syndrome, periodontal type 2; Complement component C1s deficiencyAD/AR

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)

Refs: 9856483; 9973493; 11390518; 19155518; 20191570; 27745832Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1S variants in ClinVar

10 Conditions Cataloged
not providedTotal: 620
not specifiedTotal: 121
Inborn genetic diseasesTotal: 83
C1S-related disorderTotal: 39
Ehlers-Danlos syndrome, periodontal type 2Total: 23
Complement component C1s deficiencyTotal: 16
Ehlers-Danlos syndrome, periodontal type 1Total: 2
EBV-positive nodal T- and NK-cell lymphomaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
143
clinvar
151
missense
1
clinvar
364
clinvar
17
clinvar
382
nonsense
10
clinvar
1
clinvar
11
start loss
1
clinvar
1
frameshift
15
clinvar
5
clinvar
6
clinvar
26
splice donor/acceptor (+/-2bp)
6
clinvar
6
clinvar
12
Total26133841600583

Highest pathogenic variant AF is 0.000031503525

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001734.5RefSeqNP_001725.111MANE Select
ENST00000360817.10EnsemblENSP00000354057.511MANE Select
NM_001346850.2RefSeqNP_001333779.18Standard
NM_201442.4RefSeqNP_958850.111Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5593423720.9180.00002064527
Missense (PolyPhen)100136.190.734291735
Synonymous-0.3921441381.040.000007791318
Loss of Function3.281130.50.3600.00000164381

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.0000540.000054rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.000120.00012rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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