C1QTNF2
protein-codingC1q and TNF related 2, the group of C1q and TNF related
Gene summary
Predicted to enable identical protein binding activity and signaling receptor binding activity. Predicted to be involved in regulation of lipid metabolic process. Predicted to act upstream of or within several processes, including positive regulation of D-glucose import across plasma membrane; positive regulation of fatty acid oxidation; and positive regulation of glycogen biosynthetic process. Predicted to be located in obsolete extracellular space. Predicted to be part of protein-containing complex. [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 ~22.9 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 C1QTNF2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031908.6. 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 | 54 | 1 | 55 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 55 | 1 | 0 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_114114.3 | 2 | MANE Select | |
| Ensembl | ENSP00000498651.1 | 2 | MANE Select | |
| RefSeq | NP_001353433.1 | 3 | Standard | |
| Ensembl | ENSP00000377545.3 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- activation of MAPK activity
- positive regulation of glycogen biosynthetic process
- positive regulation of fatty acid oxidation
- positive regulation of glucose import
- protein homooligomerization
Molecular Function
- signaling receptor binding
- protein binding
- identical protein binding
Cellular Component
- collagen trimer
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000393975
- Coding exons
- 3
- Length
- 22891
- Individuals with no LoFs
- 125707
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 125747
- p
- 0.000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.182 | 206 | 199 | 1.04 | 0.0000129 | 2084 |
| Missense (PolyPhen) | 68 | 64.996 | 1.0462 | 658 | ||
| Synonymous | -0.159 | 90 | 88.1 | 1.02 | 0.00000629 | 716 |
| Loss of Function | 1.09 | 6 | 9.65 | 0.622 | 5.13e-7 | 118 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000073 | 0.000062 | rare |
| Latino/Admixed American | 0.00024 | 0.00023 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.00040 | 0.00039 | rare |
| Other | 0.00020 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.144
Intolerance Scores
- LoFtool
- 0.289
- RVIS EVS
- -0.54
- RVIS percentile EVS
- 20.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.102
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |