CNBD2
protein-codingcyclic nucleotide binding domain containing 2
Gene summary
Predicted to enable cAMP binding activity. Predicted to be involved in spermatogenesis. Located in sperm midpiece. [provided by Alliance of Genome Resources, Jun 2026]
- C20orf152
- CNMPD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~76.1 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 CNBD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001365709.1. 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 | 94 | 8 | 102 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 94 | 8 | 0 | 102 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001352638.1 | 12 | MANE Select | |
| Ensembl | ENSP00000363084.3 | 12 | MANE Select | |
| RefSeq | NP_001194005.1 | 11 | Standard | |
| RefSeq | NP_001291296.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- spermatogenesis
Molecular Function
- cAMP binding
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000349339
- Coding exons
- 12
- Length
- 62111
- Individuals with no LoFs
- 125637
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 111
- Defined
- 125748
- p
- 0.000441
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.192 | 310 | 320 | 0.970 | 0.0000175 | 3800 |
| Missense (PolyPhen) | 82 | 76.751 | 1.0684 | 897 | ||
| Synonymous | 0.327 | 114 | 119 | 0.962 | 0.00000649 | 1037 |
| Loss of Function | 0.501 | 27 | 30.0 | 0.901 | 0.00000154 | 346 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0012 | 0.0012 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0011 | 0.00092 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00055 | 0.00052 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential for male fertility. Plays an important role in spermatogenesis and regulates sperm motility by controlling the development of the flagellar bending of sperm. {ECO:0000250|UniProtKB:Q9D5U8}.;
Intolerance Scores
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 62.1
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |