GCNA

gene
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Also known as NAAR1

Summary

GCNA (germ cell nuclear acidic peptidase, HGNC:15805) is a protein-coding gene on chromosome Xq13.1, encoding Germ cell nuclear acidic protein (Q96QF7). May play a role in DNA-protein cross-links (DPCs) clearance through a SUMO-dependent recruitment to sites of DPCs, ensuring the genomic stability by protecting germ cells and early embryos from various sources of damage.

Enables SUMO polymer binding activity. Involved in protein-DNA covalent cross-linking repair. Located in PML body. Implicated in X-linked spermatogenic failure 4.

Source: NCBI Gene 93953 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): spermatogenic failure, X-linked, 4 (Strong, GenCC)
  • Clinical variants (ClinVar): 184 total — 3 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 14
  • MANE Select transcript: NM_052957

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15805
Approved symbolGCNA
Namegerm cell nuclear acidic peptidase
LocationXq13.1
Locus typegene with protein product
StatusApproved
AliasesNAAR1
Ensembl geneENSG00000147174
Ensembl biotypeprotein_coding
OMIM300369
Entrez93953

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000373695, ENST00000373696, ENST00000471950, ENST00000917930

RefSeq mRNA: 1 — MANE Select: NM_052957 NM_052957

CCDS: CCDS35326

Canonical transcript exons

ENST00000373696 — 13 exons

ExonStartEnd
ENSE000009791267161235571612559
ENSE000010924447160897371609117
ENSE000010924457160566371605729
ENSE000012125527157843771578522
ENSE000012125647161286271613583
ENSE000012125747158082071580880
ENSE000014612687160358871604676
ENSE000014612727159795071598038
ENSE000016024567159212271592168
ENSE000016444207159474671594779
ENSE000017672957159433171594377
ENSE000017907937159253771592570
ENSE000035510537161068171610819

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 88.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0228 / max 12.6304, expressed in 11 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1967060.022811

Top tissues by expression

241 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.40gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.07gold quality
ileal mucosaUBERON:000033178.76gold quality
right testisUBERON:000453478.58gold quality
granulocyteCL:000009477.99gold quality
gastrocnemiusUBERON:000138877.40gold quality
spermCL:000001977.17gold quality
cartilage tissueUBERON:000241876.80gold quality
left testisUBERON:000453376.72gold quality
testisUBERON:000047376.50gold quality
muscle of legUBERON:000138376.35gold quality
hindlimb stylopod muscleUBERON:000425275.70gold quality
tibialis anteriorUBERON:000138575.41silver quality
middle temporal gyrusUBERON:000277175.12gold quality
spleenUBERON:000210673.96gold quality
cerebellar hemisphereUBERON:000224573.46gold quality
cerebellar cortexUBERON:000212973.31gold quality
deltoidUBERON:000147672.86silver quality
right hemisphere of cerebellumUBERON:001489072.67gold quality
mucosa of transverse colonUBERON:000499172.15gold quality
Brodmann (1909) area 23UBERON:001355472.15gold quality
cerebellumUBERON:000203772.03gold quality
left adrenal gland cortexUBERON:003582571.62gold quality
right lobe of liverUBERON:000111471.49gold quality
right adrenal glandUBERON:000123371.46gold quality
calcaneal tendonUBERON:000370171.37gold quality
tibial nerveUBERON:000132371.31gold quality
lower esophagus mucosaUBERON:003583471.17gold quality
right adrenal gland cortexUBERON:003582771.03gold quality
left adrenal glandUBERON:000123470.71gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting GCNA, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-369-3P99.8570.522264
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-576-5P99.8470.462582
HSA-MIR-807699.7868.521170
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-197699.7465.481127
HSA-MIR-361899.6968.571012
HSA-MIR-24-3P99.5969.971934
HSA-MIR-6727-3P99.4965.921333
HSA-MIR-448099.4266.02735
HSA-MIR-4722-3P99.3565.221099
HSA-MIR-431299.3467.30511
HSA-MIR-6739-3P99.2268.841843
HSA-MIR-6814-5P99.0366.681273
HSA-MIR-511-5P98.9770.942268
HSA-MIR-10A-5P98.8969.85712
HSA-MIR-10B-5P98.8969.86711
HSA-MIR-3074-5P98.8266.561414
HSA-MIR-942-3P98.8169.04876
HSA-MIR-770598.6967.47543
HSA-MIR-6830-3P98.6268.071760
HSA-MIR-6852-3P98.5467.601468
HSA-MIR-431798.4967.09987
HSA-MIR-4766-3P98.4867.941347
HSA-MIR-442197.9964.89701
HSA-MIR-1912-5P97.9467.98832

Literature-anchored findings (GeneRIF, showing 2)

  • Variants in GCNA, X-linked germ-cell genome integrity gene, identified in men with primary spermatogenic failure. (PMID:33963445)
  • Pathogenic variations in Germ Cell Nuclear Acidic Peptidase (GCNA) are associated with human male infertility. (PMID:34413498)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogcnaENSDARG00000101060
drosophila_melanogasterGcnaFBGN0023515
drosophila_melanogasterCG2694FBGN0024991
drosophila_melanogasterCG11322FBGN0031856
caenorhabditis_elegansWBGENE00022694

Protein

Protein identifiers

Germ cell nuclear acidic proteinQ96QF7 (reviewed: Q96QF7)

Alternative names: Acidic repeat-containing protein, Germ cell nuclear acidic peptidase, Germ cell nuclear antigen

All UniProt accessions (1): Q96QF7

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in DNA-protein cross-links (DPCs) clearance through a SUMO-dependent recruitment to sites of DPCs, ensuring the genomic stability by protecting germ cells and early embryos from various sources of damage. Can resolve the topoisomerase II (TOP2A) DPCs.

Subunit / interactions. Interacts (via SIM domains) with SUMO2; this interaction allows the GCNA recruitment to DPCs sites. Interacts with TOP2A; this interaction allows the resolution of topoisomerase II (TOP2A) DNA-protein cross-links.

Subcellular location. Nucleus. PML body. Chromosome.

Tissue specificity. Expressed in germ cells of the testis (at protein level). Detected in skeletal muscle, liver, kidney, pancreas, heart, lung and brain. Expressed throughout spermatogenesis, from spermatogonia to elongated spermatids, in normal adult testis (at protein level).

Disease relevance. Spermatogenic failure, X-linked, 4 (SPGFX4) [MIM:301077] A male infertility disorder characterized by non-obstructive azoospermia or oligoasthenoteratozoospermia. Some patients present spermatogenic maturation arrest with an almost complete absence of early and late primary spermatocytes. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. SUMO interaction motif 1 (SIM) mediates the binding to polysumoylated substrates.

Similarity. Belongs to the serine-aspartate repeat-containing protein (SDr) family.

RefSeq proteins (1): NP_443189* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006640SprT-like_domainDomain

Pfam: PF10263

UniProt features (34 total): sequence variant 18, compositionally biased region 5, short sequence motif 4, mutagenesis site 4, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96QF7-F159.130.21

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (4):

PositionPhenotype
22–25impairs sumo2 interaction. loss of sumo2 interaction; when associated with 76-a–a-79, 97-a–a-100 and 121-a–a-124. los
76–79impairs sumo2 interaction. loss of sumo2 interaction; when associated with 22-a–a-25, 97-a–a-100 and 121-a–a-124. los
97–100impairs sumo2 interaction. loss of sumo2 interaction; when associated with 22-a–a-25, 76-a–a-79 and 121-a–a-124. loss
121–124impairs sumo2 interaction. loss of sumo2 interaction; when associated with 22-a–a-25, 76-a–a-79 and 97-a–a-100. loss

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GOBP_DNA_DAMAGE_RESPONSE, GOCC_NUCLEAR_BODY, GOCC_PML_BODY, GOBP_DNA_METABOLIC_PROCESS, GOMF_UBIQUITIN_LIKE_PROTEIN_BINDING, GOBP_DNA_REPAIR, GOMF_SUMO_BINDING, SENESE_HDAC1_AND_HDAC2_TARGETS_UP, chrXq13, GOMF_SUMO_POLYMER_BINDING, STK33_SKM_UP, H1_6_TARGET_GENES, LMTK3_TARGET_GENES, ZNF184_TARGET_GENES

GO Biological Process (2): protein-DNA covalent cross-linking repair (GO:0106300), DNA damage response (GO:0006974)

GO Molecular Function (2): SUMO polymer binding (GO:0032184), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), PML body (GO:0016605)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA repair1
cellular response to stress1
SUMO binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
intracellular membraneless organelle1
nuclear body1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GCNASPRTNQ9H040745
GCNATAF1P21675560
GCNADAZLQ92904543
GCNASTRA8Q7Z7C7538
GCNASYCP3Q8IZU3523
GCNAFAM111AQ96PZ2507
GCNAFRMPD1Q5SYB0472
GCNATDP2O95551447
GCNASPO11Q9Y5K1440
GCNAFBXO21O94952429
GCNAFLAD1Q8NFF5427
GCNAELP4Q96EB1425
GCNADDX4Q9NQI0419
GCNANANOS3P60323417
GCNAUSP31Q70CQ4411

IntAct

2 interactions, top by confidence:

ABTypeScore
GCNAsphpsi-mi:“MI:0915”(physical association)0.000

BioGRID (6): SUMO2 (Affinity Capture-Western), ACRC (Affinity Capture-MS), HSP90B2P (Cross-Linking-MS (XL-MS)), HSP90B1 (Cross-Linking-MS (XL-MS)), PLCB3 (Cross-Linking-MS (XL-MS)), ACRC (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1D9BZF0, A6QL64, B4DH59, B5DUH6, D3YZV8, E9Q6E9, O43493, O46383, O77733, P06916, P08116, P0C758, P0DKJ7, P0DKJ8, P0DPF3, P31568, P62521, Q01033, Q01042, Q1HVF7, Q2W8Q7, Q3BBV2, Q42626, Q42627, Q4ZJZ1, Q4ZJZ3, Q5JPF3, Q5MJ10, Q6AXX0, Q6GX35, Q6IC83, Q6P3W6, Q6PGQ1, Q7M4S9, Q7M732, Q86T75, Q8BP27, Q8IZU1, Q8N2N9, Q96QF7

Diamond homologs: A0A0R4IWG9, O42953, Q23462, Q7KW09, Q96QF7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

184 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic3
Likely pathogenic1
Uncertain significance93
Likely benign21
Benign0

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1180854NM_052957.5(GCNA):c.1180G>T (p.Glu394Ter)Pathogenic
1328948NM_052957.5(GCNA):c.1507del (p.Glu504fs)Pathogenic
1676580NM_052957.5(GCNA):c.653_654delinsGC (p.Lys218Ser)Pathogenic
1244252NM_052957.5(GCNA):c.343del (p.Ala115fs)Likely pathogenic

SpliceAI

1917 predictions. Top by Δscore:

VariantEffectΔscore
X:71578520:CAG:Cdonor_loss1.0000
X:71578523:GTAG:Gdonor_loss1.0000
X:71578524:T:Adonor_loss1.0000
X:71592535:A:AGacceptor_gain1.0000
X:71592536:G:GGacceptor_gain1.0000
X:71592536:GCT:Gacceptor_gain1.0000
X:71594744:A:AGacceptor_gain1.0000
X:71594745:G:GGacceptor_gain1.0000
X:71594745:GCT:Gacceptor_gain1.0000
X:71598012:C:Gdonor_gain1.0000
X:71603587:GATGA:Gacceptor_gain1.0000
X:71605652:ATCT:Aacceptor_gain1.0000
X:71605655:T:TAacceptor_gain1.0000
X:71608969:GCAGG:Gacceptor_loss1.0000
X:71608970:CA:Cacceptor_loss1.0000
X:71608971:A:ACacceptor_loss1.0000
X:71608971:A:AGacceptor_gain1.0000
X:71608971:AG:Aacceptor_gain1.0000
X:71608972:G:GTacceptor_gain1.0000
X:71608972:GG:Gacceptor_gain1.0000
X:71609113:AAAAG:Adonor_loss1.0000
X:71609114:AAAGG:Adonor_loss1.0000
X:71609116:AGGTA:Adonor_loss1.0000
X:71609118:G:Adonor_loss1.0000
X:71609119:T:Adonor_loss1.0000
X:71612349:TTCAA:Tacceptor_loss1.0000
X:71612350:TCAAG:Tacceptor_loss1.0000
X:71612351:CAA:Cacceptor_loss1.0000
X:71612352:A:AGacceptor_gain1.0000
X:71612352:AAGA:Aacceptor_loss1.0000

AlphaMissense

4697 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:71609001:T:CF499L0.953
X:71609003:C:AF499L0.953
X:71609003:C:GF499L0.953
X:71612406:T:CL601P0.951
X:71610777:T:CF570L0.930
X:71610779:T:AF570L0.930
X:71610779:T:GF570L0.930
X:71610705:T:AW546R0.923
X:71610705:T:CW546R0.923
X:71612474:C:GH624D0.915
X:71612476:C:AH624Q0.915
X:71612476:C:GH624Q0.915
X:71610787:T:CI573T0.914
X:71612402:T:AW600R0.911
X:71612402:T:CW600R0.911
X:71612899:T:CF665L0.911
X:71612901:C:AF665L0.911
X:71612901:C:GF665L0.911
X:71609089:T:CL528P0.910
X:71609068:T:CL521S0.903
X:71610707:G:CW546C0.898
X:71610707:G:TW546C0.898
X:71609005:T:CL500S0.897
X:71612404:G:CW600C0.889
X:71612404:G:TW600C0.889
X:71612540:T:AC646S0.889
X:71612541:G:CC646S0.889
X:71612443:G:CW613C0.888
X:71612443:G:TW613C0.888
X:71609100:T:CS532P0.886

dbSNP variants (sampled 300 via entrez): RS1000167614 (X:71593174 G>A), RS1000545918 (X:71596569 T>C), RS1000605059 (X:71577782 C>CT), RS1000681564 (X:71597479 G>A), RS1000687217 (X:71581225 A>G), RS1000873953 (X:71604985 G>A), RS1000977475 (X:71607899 G>A), RS1001030161 (X:71596153 T>G), RS1001164776 (X:71581934 C>T), RS1001169665 (X:71589717 G>A), RS1001269447 (X:71605553 T>C), RS1001307009 (X:71588769 G>C), RS1001470472 (X:71601758 C>T), RS1001744318 (X:71602071 C>T), RS1002302565 (X:71598494 G>A)

Disease associations

OMIM: gene MIM:300369 | disease phenotypes: MIM:301077

GenCC curated gene-disease

DiseaseClassificationInheritance
spermatogenic failure, X-linked, 4StrongX-linked

Mondo (2): spermatogenic failure, X-linked, 4 (MONDO:0024773), azoospermia (MONDO:0100459)

Orphanet (0):

HPO phenotypes

14 total (14 of 14 shown, HPO-id order):

HPOTerm
HP:0000027Azoospermia
HP:0000118Phenotypic abnormality
HP:0000837Increased circulating gonadotropin level
HP:0001417X-linked inheritance
HP:0003251Male infertility
HP:0008232Elevated circulating follicle stimulating hormone level
HP:0008669Abnormal spermatogenesis
HP:0008734Decreased testicular size
HP:0011462Young adult onset
HP:0011961Non-obstructive azoospermia
HP:0011962Obstructive azoospermia
HP:0011969Elevated circulating luteinizing hormone level
HP:0040086Abnormal prolactin level
HP:0040171Decreased serum testosterone concentration

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D053713AzoospermiaC12.100.500.430.380; C12.100.750.700.380; C12.200.294.430.380

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
methylmercuric chlorideincreases expression3
mercuric bromideincreases expression, affects cotreatment2
Benzo(a)pyreneincreases expression2
Tobacco Smoke Pollutionincreases expression2
Valproic Acidincreases expression, increases methylation2
Cyclosporineincreases expression2
aristolochic acid Iincreases expression1
bisphenol Adecreases expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
2-butenalincreases expression1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
ochratoxin Aincreases expression1
cupric oxideincreases expression1
di-n-butylphosphoric acidaffects expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
torcetrapibincreases expression1
dorsomorphinaffects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1
PCI 5002affects cotreatment, increases expression1
theaflavin-3,3’-digallateaffects expression1
Air Pollutantsdecreases expression, increases abundance1
Hexachlorocyclohexaneincreases expression1
Copperaffects binding, decreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Demecolcineincreases expression1
Disulfiramaffects binding, decreases expression1
Drugs, Chinese Herbalincreases expression1
Formaldehydeincreases expression1

Clinical trials (associated diseases)

27 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT02307994PHASE4UNKNOWNClinical Research on Effectiveness and Safety of Treatment of Severe Oligospermia or Azoospermia With uFSH
NCT02275169PHASE3UNKNOWNFSH Treatment for Non-obstructive Azoospermic Patients
NCT02544191PHASE2UNKNOWNGnRHa Combined With hCG and hMG for Treatment of Patients With Non-obstructive Azoospermia
NCT03762967PHASE2UNKNOWNAutologous Adipose-Derived Adult Stromal Vascular Cell Administration for Male Patients With Infertility
NCT02041910PHASE1/PHASE2UNKNOWNTesticular Injection of Autologous Stem Cells for Treatment of Patients With Azoospermia
NCT00282477Not specifiedUNKNOWNTrial to Evaluate Erectile Function, Fertility and Sperm Count in Male Cyclists Compared to Age Matched Controls
NCT00484081Not specifiedCOMPLETEDMicrodissection Testicular Sperm Extraction (MicroTESE) and IVF-ICSI Outcome in Non-Obstructive Azoospermia (NOA)
NCT00548977Not specifiedCOMPLETEDGenetic Studies Spermatogenic Failure
NCT01375062Not specifiedCOMPLETEDObtaining Undifferentiated Cells From Testis Biopsy
NCT01509482Not specifiedCOMPLETEDInsulin Resistance in Idiopathic Oligospermia and Azoospermia
NCT02008799Not specifiedUNKNOWNIntra Testicular Artery Injection of Bone Marrow Stem Cell in Management of Azoospermia
NCT02339272Not specifiedCOMPLETEDStudy of Synapsis and Recombination in Male Meiosis and the Implications in Infertility
NCT02414295Not specifiedCOMPLETEDSperm Production in Kleinfelter Syndrome Patients After Mesenchymal Stem Cell Injection
NCT02418832Not specifiedRECRUITINGTestis Needle Aspiration of Sperm in Men With Azoospermia
NCT02617173Not specifiedUNKNOWNThe Effect of Low Electrical Current on Testicular Spermatocyte Count
NCT02773498Not specifiedTERMINATEDComparison of Medical Results of Testicular Sperm Extraction by Conventional Surgery and Microsurgical Track
NCT03497728Not specifiedTERMINATEDDetection of Microdeletions in the Azoospermia Factor (AZF) Regions in Infertile Male Patients
NCT04675164Not specifiedCOMPLETEDLaser Assisted Sperm Selection of Viable Immotile Testicular Sperm in Azoospermic Infertile Men
NCT05479474Not specifiedRECRUITINGPlatelet Rich Plasma Testis Treatment for Infertile Men
NCT05628987Not specifiedRECRUITINGThe Association of Gut Microbiota and Spermatogenic Dysfunction
NCT05866484Not specifiedCOMPLETEDTesticular Sperm Aspiration (TESA) vs. Microfluidic Sperm Separation (MSS)
NCT06524258Not specifiedCOMPLETEDTesticular Elastography for Microscopic Testicular Sperm Extraction
NCT06841328Not specifiedRECRUITINGFertility Enhancement Through Regenerative Treatment in Ovaries and Testes
NCT06941922Not specifiedRECRUITINGTesticular Evaluation of Azoospermia Using Micro-Ultrasound
NCT07074015Not specifiedRECRUITINGIntelliWell: An AI-Assisted Imaging Platform for Detection and Location of Ultra-Rare Testicular Sperm in Surgical Specimens
NCT07357701Not specifiedRECRUITINGIdentifying Genome Variants in Non-Obstructive Azoospermia (NOA) or Primary Ovarian Insufficiency (POI)
NCT07542626Not specifiedRECRUITINGFertility Restoration With Autografting of Cryopreserved Immature Testicular Tissue