HJURP
protein-codingHolliday junction recognition protein
Gene summary
Enables histone binding activity and identical protein binding activity. Involved in CENP-A containing chromatin assembly; chromosome segregation; and regulation of protein-containing complex assembly. Located in kinetochore and nucleolus. [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 ~21.2 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 HJURP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018410.5. 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 | 114 | 21 | 135 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 118 | 22 | 0 | 140 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060880.3 | 9 | MANE Select | |
| Ensembl | ENSP00000414109.1 | 9 | MANE Select | |
| RefSeq | NP_001269891.1 | 7 | Standard | |
| RefSeq | NP_001269892.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nucleosome assembly
- Chromosome Maintenance
- Deposition of new CENPA-containing nucleosomes at the centromere
- Cell Cycle
Biological Process
- cell cycle
- chromosome segregation
- CENP-A containing nucleosome assembly
- regulation of protein complex assembly
- regulation of DNA binding
Molecular Function
- DNA binding
- protein binding
- histone binding
- identical protein binding
Cellular Component
- chromosome, centromeric region
- condensed chromosome kinetochore
- nucleus
- nucleoplasm
- nucleolus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000411486
- Coding exons
- 9
- Length
- 21151
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125748
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.296 | 442 | 425 | 1.04 | 0.0000236 | 4846 |
| Missense (PolyPhen) | 92 | 101.4 | 0.90732 | 1265 | ||
| Synonymous | 0.236 | 160 | 164 | 0.977 | 0.00000952 | 1476 |
| Loss of Function | 2.49 | 16 | 30.9 | 0.517 | 0.00000156 | 391 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Centromeric protein that plays a central role in the incorporation and maintenance of histone H3-like variant CENPA at centromeres. Acts as a specific chaperone for CENPA and is required for the incorporation of newly synthesized CENPA molecules into nucleosomes at replicated centromeres. Prevents CENPA-H4 tetramerization and prevents premature DNA binding by the CENPA-H4 tetramer. Directly binds Holliday junctions. {ECO:0000269|PubMed:19410544, ECO:0000269|PubMed:19410545}.;
Recessive Scores
- pRec
- 0.0664
Intolerance Scores
- LoFtool
- 0.774
- RVIS EVS
- 1.38
- RVIS percentile EVS
- 94.62
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.0302
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |