C1QTNF3
protein-codingC1q and TNF related 3, the group of C1q and TNF related
Gene summary
Enables identical protein binding activity. Involved in several processes, including intracellular triglyceride homeostasis; negative regulation of non-canonical NF-kappaB signal transduction; and regulation of cytokine production. Acts upstream of or within negative regulation of gluconeogenesis. Located in extracellular exosome and membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.4 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 C1QTNF3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_181435.6. 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 | 1 | 1 | ||||
| missense | 34 | 1 | 35 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 2 | 0 | 36 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_852100.3 | 6 | MANE Select | |
| Ensembl | ENSP00000371497.3 | 6 | MANE Select | |
| RefSeq | NP_112207.1 | 6 | Standard | |
| Ensembl | ENSP00000231338.7 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cellular triglyceride homeostasis
- fat cell differentiation
- negative regulation of gluconeogenesis
- positive regulation of cytokine secretion
- negative regulation of inflammatory response
Molecular Function
- molecular_function
Cellular Component
- collagen trimer
- cell
- membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000382065
- Coding exons
- 6
- Length
- 24385
- Individuals with no LoFs
- 125554
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 194
- Defined
- 125748
- p
- 0.000772
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.10 | 139 | 180 | 0.770 | 0.00000939 | 2118 |
| Missense (PolyPhen) | 57 | 72.352 | 0.78781 | 821 | ||
| Synonymous | -0.355 | 73 | 69.2 | 1.05 | 0.00000377 | 612 |
| Loss of Function | 0.757 | 12 | 15.2 | 0.790 | 8.60e-7 | 160 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.0041 | 0.0041 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00038 | 0.00038 | rare |
| South Asian | 0.0031 | 0.0031 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.314
Intolerance Scores
- LoFtool
- 0.434
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |