FOXL2NB
protein-codingFOXL2 neighbor
Gene summary
Located in fibrillar center. [provided by Alliance of Genome Resources, Jul 2025]
- C3orf72
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.8 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 FOXL2NB variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001040061.3. 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 | 25 | 2 | 27 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 2 | 0 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001035150.1 | 3 | MANE Select | |
| Ensembl | ENSP00000372651.3 | 3 | MANE Select | |
| Ensembl | ENSP00000418272.1 | 2 | Standard | |
| Ensembl | ENSP00000629904.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- fibrillar center
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000383165
- Coding exons
- 3
- Length
- 6218
- Individuals with no LoFs
- 124704
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 124705
- p
- 0.00000401
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.227 | 94 | 100 | 0.936 | 0.00000460 | 1071 |
| Missense (PolyPhen) | 39 | 35.383 | 1.1022 | 349 | ||
| Synonymous | 0.108 | 44 | 44.9 | 0.979 | 0.00000212 | 412 |
| Loss of Function | -1.28 | 5 | 2.72 | 1.84 | 1.14e-7 | 36 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.68
- RVIS percentile EVS
- 84.81
Essentials
- Essential (gene trap)
- N