RAD21L1
protein-codingRAD21 cohesin complex component like 1, the group of Kleisins
Gene summary
Predicted to enable chromatin binding activity. Predicted to be involved in replication-born double-strand break repair via sister chromatid exchange and sister chromatid cohesion. Predicted to be located in chromosome and nucleus. Predicted to be part of meiotic cohesin 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 ~70.4 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 RAD21L1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001384355.1. 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 | 62 | 4 | 1 | 67 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 1 | 0 | 64 | 4 | 1 | 70 |
Highest pathogenic variant AF is 0.0000014304248
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001371284.1 | 13 | MANE Select | |
| Ensembl | ENSP00000507397.1 | 13 | MANE Select | |
| RefSeq | NP_001130038.2 | 13 | Standard | |
| RefSeq | NP_001371285.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- double-strand break repair via homologous recombination
- double-strand break repair
- sister chromatid cohesion
- synaptonemal complex assembly
- spermatogenesis
Molecular Function
- chromatin binding
Cellular Component
- lateral element
- nucleus
- chromosome
- meiotic cohesin complex
- nuclear meiotic cohesin complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000409241
- Coding exons
- 13
- Length
- 70366
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.39 | 177 | 237 | 0.747 | 0.0000109 | 3707 |
| Missense (PolyPhen) | 43 | 72.145 | 0.59602 | 1143 | ||
| Synonymous | 1.76 | 58 | 77.8 | 0.746 | 0.00000351 | 963 |
| Loss of Function | 2.36 | 13 | 26.0 | 0.500 | 0.00000148 | 380 |
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 | 0.0 | absent |
| 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:
- Function
- FUNCTION: Meiosis-specific component of some cohesin complex required during the initial steps of prophase I in male meiosis. Probably required during early meiosis in males for separation of sister chromatids and homologous chromosomes. Replaces RAD21 in premeiotic S phase (during early stages of prophase I), while RAD21 reappears in later stages of prophase I. Involved in synaptonemal complex assembly, synapsis initiation and crossover recombination between homologous chromosomes during prophase I (By similarity). {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- 0.77
- RVIS percentile EVS
- 86.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0837
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | High | High |