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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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GCNA
germ cell nuclear acidic peptidase
Chromosome X · Xq13.1
NCBI Gene: 93953Ensembl: ENSG00000147174.13HGNC: HGNC:15805UniProt: Q96QF7
12PubMed Papers
21Diseases
0Drugs
4Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingSUMO polymer bindingnucleusnucleoplasmspermatogenic failure, X-linked, 4azoospermiamale infertility with azoospermia or oligozoospermia due to single gene mutationmale infertility
✦AI Summary

GCNA (germ cell nuclear acidic peptidase) is a conserved protease essential for protecting germ cell genome integrity. It contains an acidic intrinsically disordered region and a protease-like SprT domain that work synergistically to maintain genomic stability 1. GCNA's primary function is clearing DNA-protein crosslinks (DPCs), particularly those generated by topoisomerase II, through SUMO-dependent recruitment to damage sites 2. This DPC proteolysis mechanism operates in parallel with the related protease Spartan to digest protein components covalently attached to DNA 13. By resolving these bulky DNA lesions, GCNA prevents replication stress and chrX instability that would otherwise compromise germ cell viability 1. GCNA deficiency causes male infertility through spermatogenic failure; hemizygous GCNA mutations were identified in individuals with non-obstructive azoospermia, and notably, all patients with meiotic gene defects including GCNA had unsuccessful sperm retrieval 4. This conservation across species—from flies to humans—underscores GCNA's critical role in protecting germ cell genomes across generations 1. Clinically, GCNA mutations represent an identifiable genetic cause of X-linked male infertility, enabling better prognostic assessment for assisted reproductive procedures.

Sources cited
1
GCNA is a conserved protease containing an acidic IDR and SprT domain that protects germ cells from DNA damage and DPC accumulation
PMID: 31839537
2
GCNA is a protease implicated in topoisomerase DNA-protein crosslink resolution
PMID: 39180935
3
GCNA functions as a DPC protease involved in genome stability and DNA repair
PMID: 33398053
4
Hemizygous GCNA mutations cause non-obstructive azoospermia and are associated with unsuccessful sperm retrieval in meiotic gene defects
PMID: 35172124
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ21
spermatogenic failure, X-linked, 4Open Targets
0.47Moderate
azoospermiaOpen Targets
0.45Moderate
male infertility with azoospermia or oligozoospermia due to single gene mutationOpen Targets
0.37Weak
male infertilityOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.01Suggestive
endocarditisOpen Targets
0.01Suggestive
teratomaOpen Targets
0.01Suggestive
cancerOpen Targets
0.01Suggestive
acute myeloid leukemiaOpen Targets
0.01Suggestive
infertilityOpen Targets
0.01Suggestive
germ cell tumorOpen Targets
0.00Suggestive
Ewing sarcomaOpen Targets
0.00Suggestive
type 2 diabetes mellitusOpen Targets
0.00Suggestive
adrenal cortex carcinomaOpen Targets
0.00Suggestive
Familial prostate cancerOpen Targets
0.00Suggestive
hereditary breast carcinomaOpen Targets
0.00Suggestive
melanomaOpen Targets
0.00Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.00Suggestive
ThymomaOpen Targets
0.00Suggestive
thyroid cancer, nonmedullary, 1Open Targets
0.00Suggestive
Spermatogenic failure, X-linked, 4UniProt
Pathogenic Variants4
NM_052957.5(GCNA):c.343del (p.Ala115fs)Likely pathogenic
Non-obstructive azoospermia|Spermatogenic failure, X-linked, 4
★☆☆☆2022→ Residue 115
NM_052957.5(GCNA):c.1180G>T (p.Glu394Ter)Pathogenic
Non-obstructive azoospermia|Spermatogenic failure, X-linked, 4
☆☆☆☆2022→ Residue 394
NM_052957.5(GCNA):c.1507del (p.Glu504fs)Pathogenic
Azoospermia|Spermatogenic failure, X-linked, 4
☆☆☆☆2022→ Residue 504
NM_052957.5(GCNA):c.653_654delinsGC (p.Lys218Ser)Pathogenic
Spermatogenic failure, X-linked, 4
☆☆☆☆2022→ Residue 218
View on ClinVar ↗
Related Genes
SPRTNProtein interaction76%SPINDOCShared pathway50%FLYWCH1Shared pathway50%DCPH1Shared pathway50%ZBTB4Shared pathway50%SUSD6Shared pathway50%
Tissue Expression6 tissues
Liver
100%
Lung
87%
Bone Marrow
79%
Ovary
66%
Heart
47%
Brain
24%
Gene Interaction Network
Click a node to explore
GCNASPRTNSPINDOCFLYWCH1DCPH1ZBTB4SUSD6
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q96QF7
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.20Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.08 [0.04–0.20]
RankingsWhere GCNA stands among ~20K protein-coding genes
  • #16,460of 20,598
    Most Researched12
  • #3,877of 5,498
    Most Pathogenic Variants4
  • #448of 17,882
    Most Constrained (LOEUF)0.20 · top 5%
Genes detectedGCNA
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Whole-exome sequencing improves the diagnosis and care of men with non-obstructive azoospermia.
PMID: 35172124
Am J Hum Genet · 2022
1.00
2
Autophagy regulation and protein kinase activity of PIK3C3 controls sertoli cell polarity through its negative regulation on SCIN (scinderin).
PMID: 37450577
Autophagy · 2023
0.90
3
From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks.
PMID: 39180935
DNA Repair (Amst) · 2024
0.80
4
GCNA Preserves Genome Integrity and Fertility Across Species.
PMID: 31839537
Dev Cell · 2020
0.70
5
DNA-protein crosslink proteases in genome stability.
PMID: 33398053
Commun Biol · 2021
0.60