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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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H3-5
H3.5 histone
Chromosome 12 · 12p11.21
NCBI Gene: 440093Ensembl: ENSG00000188375.5HGNC: HGNC:33164UniProt: Q6NXT2
49PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
euchromatinnucleosomal DNA bindingprotein bindingpositive regulation of cell growthovarian neoplasmAlzheimer diseaseamyotrophic lateral sclerosisazoospermia
✦AI Summary

H3.5 is a hominid-specific histone H3 variant encoded on chromosome 12.21 that functions as a core nucleosomal component 1. As a variant histone, H3.5 participates in chr12 organization and DNA packaging alongside canonical histones, contributing to transcription regulation, DNA repair, and chr12 stability 2. Structurally, H3.5 forms an unstable nucleosome compared to H3.3 due to a histone-specific Leu103 residue that reduces hydrophobic interactions with histone H4, enabling dynamic chr12 remodeling around transcription start sites 3. H3.5 preferentially colocalizes with euchromatin and associates with actively transcribed genes 1. In testicular tissue, H3.5 is primarily enriched in spermatocytes and plays roles in DNA synthesis during normal spermatogenesis; expression correlates positively with proliferating cell nuclear antigen (PCNA) 4. Reduced H3.5 expression occurs in patients with non-obstructive azoospermia, and expression is regulated by gonadotropins 4. At the protein level, H3.5 interacts with multiple histone chaperones including Asf1a, Asf1b, HIRA, CAF p150, and DAXX 5. Disease relevance includes potential associations with testicular tumors, as elevated H3.5 expression and copy number gains were observed in seminoma specimens 5. H3.5 is identified as a cancer-associated gene in pan-cancer analyses 6.

Sources cited
1
H3.5 is a hominid-specific histone H3 variant encoded on chromosome 12, preferentially colocalizes with euchromatin, associates with actively transcribed genes
PMID: 21274551
2
H3.5 is unique to primates/Hominidae and functions as a histone variant with distinct roles from canonical histones
PMID: 33245240
3
H3.5 nucleosome is less stable than H3.3 due to Leu103 residue, accumulates around transcription start sites in testicular cells
PMID: 26779285
4
H3.5 is highly expressed in human testis, primarily in spermatocytes; its expression correlates with PCNA and DNA synthesis, is reduced in non-obstructive azoospermia, and is regulated by gonadotropins
PMID: 29179259
5
H3.5 is enriched in spermatocytes, regulated by DNA methylation at the promoter, elevated in seminoma specimens with copy number gains, and interacts with histone chaperones Asf1a, Asf1b, HIRA, CAF p150, and DAXX
PMID: 39702777
6
H3F3C (H3.5) is identified as a cancer-associated gene in pan-cancer analyses
PMID: 31221981
Disease Associationsⓘ20
ovarian neoplasmOpen Targets
0.33Weak
Alzheimer diseaseOpen Targets
0.24Weak
amyotrophic lateral sclerosisOpen Targets
0.22Weak
azoospermiaOpen Targets
0.08Suggestive
diabetes mellitusOpen Targets
0.06Suggestive
spermatogenic failure 61Open Targets
0.06Suggestive
spermatogenic failure 62Open Targets
0.06Suggestive
spermatogenic failure 88Open Targets
0.06Suggestive
spermatogenic failure 59Open Targets
0.06Suggestive
spermatogenic failure 60Open Targets
0.06Suggestive
spermatogenic failure 73Open Targets
0.06Suggestive
spermatogenic failure 74Open Targets
0.06Suggestive
partial chromosome Y deletionOpen Targets
0.06Suggestive
spermatogenic failure 48Open Targets
0.06Suggestive
spermatogenic failure 20Open Targets
0.06Suggestive
spermatogenic failure 72Open Targets
0.06Suggestive
spermatogenic failure 18Open Targets
0.06Suggestive
spermatogenic failure 27Open Targets
0.06Suggestive
spermatogenic failure 46Open Targets
0.06Suggestive
spermatogenic failure 49Open Targets
0.06Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ATRXProtein interaction100%BRDTProtein interaction100%CHD4Protein interaction100%DNMT1Protein interaction100%DNMT3AProtein interaction100%DNMT3BProtein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
5%
Ovary
1%
Lung
0%
Brain
0%
Liver
0%
Gene Interaction Network
Click a node to explore
H3-5ATRXBRDTCHD4DNMT1DNMT3ADNMT3B
PROTEIN STRUCTURE
Preparing viewer…
PDB8T4R · 1.20 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.69LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.01 [0.60–1.69]
RankingsWhere H3-5 stands among ~20K protein-coding genes
  • #8,949of 20,598
    Most Researched49
  • #16,072of 17,882
    Most Constrained (LOEUF)1.69
Genes detectedH3-5
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Primate-specific histone variants.
PMID: 33245240
Genome · 2021
1.00
2
The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism.
PMID: 31221981
Exp Mol Med · 2019
0.90
3
Roles of histone H3.5 in human spermatogenesis and spermatogenic disorders.
PMID: 29179259
Andrology · 2018
0.80
4
Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis.
PMID: 26779285
Epigenetics Chromatin · 2016
0.70
5
Histone variant H3.5 in testicular cell differentiation and its interactions with histone chaperones.
PMID: 39702777
Sci Rep · 2024
0.60