C1QL1
protein-codingcomplement C1q like 1, the group of C1q and TNF related
Gene summary
Predicted to enable signaling receptor binding activity. Predicted to be involved in maintenance of synapse structure and trans-synaptic signaling, modulating synaptic transmission. Predicted to act upstream of or within motor learning and neuron remodeling. Predicted to be located in several cellular components, including climbing fiber; extracellular region; and presynapse. Predicted to be active in obsolete extracellular space; synapse; and synaptic cleft. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.6 kbGenCC 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 C1QL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006688.5. 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 | 0 | |||||
| missense | 40 | 1 | 41 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 1 | 0 | 42 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006679.1 | 2 | MANE Select | |
| Ensembl | ENSP00000253407.2 | 2 | MANE Select | |
| Ensembl | ENSP00000520823.1 | 2 | Standard | |
| Ensembl | ENSP00000520823.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- locomotory behavior
- neuron remodeling
- motor learning
- maintenance of synapse structure
Molecular Function
- molecular_function
- signaling receptor binding
- protein binding
Cellular Component
- cellular_component
- collagen trimer
- cytoplasm
- synaptic cleft
- climbing fiber
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000253407
- Coding exons
- 2
- Length
- 8379
- Individuals with no LoFs
- 125697
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125715
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 96 | 137 | 0.699 | 0.00000684 | 1655 |
| Missense (PolyPhen) | 34 | 58.006 | 0.58615 | 626 | ||
| Synonymous | 1.34 | 50 | 63.6 | 0.787 | 0.00000368 | 553 |
| Loss of Function | -0.719 | 7 | 5.23 | 1.34 | 2.23e-7 | 64 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May regulate the number of excitatory synapses that are formed on hippocampus neurons. Has no effect on inhibitory synapses (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.122
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.336
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |