RHNO1
protein-codingRAD9-HUS1-RAD1 interacting nuclear orphan 1
Gene summary
Enables chromatin-protein adaptor activity. Involved in several processes, including DNA repair; cellular response to radiation; and regulation of cell cycle process. Located in chromosome and nucleus. Is active in chromatin and site of double-strand break. [provided by Alliance of Genome Resources, Jul 2025]
- C12orf32
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.3 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 RHNO1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001252499.3. 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 | 1 | 1 | ||||
| missense | 1 | 1 | 2 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 2 | 2 | 0 | 4 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001239428.1 | 2 | MANE Select | |
| Ensembl | ENSP00000438590.1 | 2 | MANE Select | |
| RefSeq | NP_001239429.1 | 2 | Standard | |
| RefSeq | NP_001244026.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- HDR through Single Strand Annealing (SSA)
- HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
- DNA Repair
- Gene expression (Transcription)
- DNA Double-Strand Break Repair
Biological Process
- DNA damage checkpoint
- recombinational repair
- cell cycle
- cellular response to UV
- positive regulation of G0 to G1 transition
Molecular Function
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- chromosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000489288
- Coding exons
- 2
- Length
- 13203
- Individuals with no LoFs
- 125364
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 382
- Defined
- 125748
- p
- 0.00153
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0186 | 127 | 128 | 0.995 | 0.00000636 | 1529 |
| Missense (PolyPhen) | 34 | 35.17 | 0.96672 | 449 | ||
| Synonymous | 0.329 | 46 | 48.9 | 0.940 | 0.00000234 | 486 |
| Loss of Function | 1.08 | 5 | 8.39 | 0.596 | 4.85e-7 | 94 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.0043 | 0.0043 | notable |
| European (Non-Finnish) | 0.0021 | 0.0021 | notable |
| South Asian | 0.00027 | 0.00026 | rare |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in DNA damage response (DDR) signaling upon genotoxic stresses such as ionizing radiation (IR) during the S phase. Recruited to sites of DNA damage through interaction with the 9-1-1 cell-cycle checkpoint response complex and TOPBP1 in a ATR-dependent manner. Required for the progression of the G1 to S phase transition. Plays a role in the stimulation of CHEK1 phosphorylation. {ECO:0000269|PubMed:21659603}.;
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 | Medium |
| Cancer | Medium | Medium | Medium |