HJURP

Holliday junction recognition protein

Basic information

Region (hg38): 2:233833416-233854566

Links

ENSG00000123485 ∙ NCBI:55355 ∙ OMIM:612667 ∙ HGNC:25444 ∙ Uniprot:Q8NCD3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HJURP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HJURP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			49	8		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	9	0

Variants in HJURP

This is a list of pathogenic ClinVar variants found in the HJURP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-233837625-T-G		not specified	Uncertain significance (Jul 19, 2023)
2-233837641-G-A		not specified	Uncertain significance (Apr 08, 2023)
2-233837643-G-C		not specified	Uncertain significance (Jan 10, 2023)
2-233840611-C-A		not specified	Uncertain significance (Nov 12, 2024)
2-233840636-C-T		not specified	Uncertain significance (Nov 15, 2024)
2-233840658-C-A		not specified	Uncertain significance (Nov 09, 2024)
2-233840678-G-A		not specified	Uncertain significance (Jul 27, 2024)
2-233840682-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-233840721-C-T		not specified	Uncertain significance (Sep 30, 2024)
2-233840766-C-T		not specified	Uncertain significance (Dec 20, 2021)
2-233840943-T-C		not specified	Uncertain significance (Mar 31, 2024)
2-233840970-A-C		not specified	Uncertain significance (Dec 19, 2022)
2-233840970-A-G		not specified	Uncertain significance (Jul 14, 2022)
2-233840987-T-G		not specified	Uncertain significance (Jun 12, 2023)
2-233841005-C-T		not specified	Uncertain significance (Feb 06, 2024)
2-233841032-T-A		not specified	Uncertain significance (Aug 14, 2024)
2-233841048-C-T		not specified	Uncertain significance (Nov 12, 2024)
2-233841063-C-T		not specified	Likely benign (Jun 07, 2024)
2-233841102-T-C		not specified	Uncertain significance (Jan 09, 2023)
2-233841114-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-233841150-C-T		not specified	Uncertain significance (Nov 08, 2022)
2-233841173-G-A		not specified	Uncertain significance (Jul 16, 2024)
2-233841176-C-A		not specified	Uncertain significance (Aug 01, 2024)
2-233841176-C-T		not specified	Likely benign (Feb 10, 2022)
2-233841177-G-A		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HJURP	protein_coding	protein_coding	ENST00000411486	9	21151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.05e-7	0.994	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	442	425	1.04	0.0000236	4846
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Nucleosome assembly;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.0664

Intolerance Scores

• loftool: 0.774
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.62

Haploinsufficiency Scores

• pHI: 0.539
• hipred: N
• hipred_score: 0.485
• ghis: 0.518

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0302

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hjurp

Gene ontology

• Biological process: cell cycle;chromosome segregation;CENP-A containing nucleosome assembly;regulation of protein complex assembly;regulation of DNA binding
• Cellular component: chromosome, centromeric region;condensed chromosome kinetochore;nucleus;nucleoplasm;nucleolus;mitochondrion;cytosol
• Molecular function: DNA binding;protein binding;histone binding;identical protein binding