NXNL2
protein-codingnucleoredoxin like 2, the group of Nucleoredoxin family
Gene summary
Predicted to be involved in sensory perception of smell and visual perception. [provided by Alliance of Genome Resources, Jul 2025]
- C9orf121
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.2 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 NXNL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001161625.2. 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 | 25 | 2 | 27 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 26 | 2 | 0 | 28 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001155097.1 | 2 | MANE Select | |
| Ensembl | ENSP00000365014.3 | 2 | MANE Select | |
| RefSeq | NP_660326.2 | 2 | Standard | |
| Ensembl | ENSP00000365015.3 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- visual perception
- sensory perception of smell
- photoreceptor cell maintenance
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375854
- Coding exons
- 2
- Length
- 49174
- Individuals with no LoFs
- 124304
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 124315
- p
- 0.0000442
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.167 | 98 | 93.5 | 1.05 | 0.00000472 | 994 |
| Missense (PolyPhen) | 36 | 30.461 | 1.1819 | 325 | ||
| Synonymous | -0.733 | 50 | 43.8 | 1.14 | 0.00000235 | 329 |
| Loss of Function | 1.78 | 0 | 3.69 | 0.00 | 1.57e-7 | 43 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00042 | 0.00037 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000028 | 0.000027 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in the maintenance of both the function and the viability of sensory neurons, including photoreceptors and olfactory neurons. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- LoFtool
- 0.316
- RVIS EVS
- 0.35
- RVIS percentile EVS
- 73.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.437
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |