GNL1

gene
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Also known as HSR1

Summary

GNL1 (G protein nucleolar 1, HGNC:4413) is a protein-coding gene on chromosome 6p21.33, encoding Guanine nucleotide-binding protein-like 1 (P36915). Possible regulatory or functional link with the histocompatibility cluster.

The GNL1 gene, identified in the human major histocompatibility complex class I region, shows a high degree of similarity with its mouse counterpart. The GNL1 gene is located less than 2 kb centromeric to HLA-E, in the same transcriptional orientation. GNL1 is telomeric to HLA-B and HLA-C.

Source: NCBI Gene 2794 — RefSeq curated summary.

At a glance

  • GWAS associations: 22
  • Clinical variants (ClinVar): 78 total
  • MANE Select transcript: NM_005275

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4413
Approved symbolGNL1
NameG protein nucleolar 1
Location6p21.33
Locus typegene with protein product
StatusApproved
AliasesHSR1
Ensembl geneENSG00000204590
Ensembl biotypeprotein_coding
OMIM143024
Entrez2794

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 3 retained_intron

ENST00000376621, ENST00000433809, ENST00000462708, ENST00000464231, ENST00000487166, ENST00000863388, ENST00000911424, ENST00000911425, ENST00000911426, ENST00000911427, ENST00000911428, ENST00000911429, ENST00000958484

RefSeq mRNA: 1 — MANE Select: NM_005275 NM_005275

CCDS: CCDS4680

Canonical transcript exons

ENST00000376621 — 12 exons

ExonStartEnd
ENSE000016444973055246730552661
ENSE000016482693054669630546836
ENSE000016571093055555530555720
ENSE000016643953055505530555191
ENSE000016704233055476430554915
ENSE000016804423055308430553179
ENSE000017690733055457530554646
ENSE000019323623054138130546313
ENSE000019522533055613130556489
ENSE000022067613055335030553557
ENSE000035189543054735230547530
ENSE000036164763054711230547274

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.0773 / max 177.2784, expressed in 1820 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
725317.24241763
725336.38061722
725305.79051684
725363.99241420
725343.12321420
725322.96511370
725290.5167280
725350.066519

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453497.36gold quality
left testisUBERON:000453397.34gold quality
stromal cell of endometriumCL:000225597.21gold quality
left ovaryUBERON:000211996.88gold quality
ovaryUBERON:000099296.77gold quality
endocervixUBERON:000045896.59gold quality
right ovaryUBERON:000211896.59gold quality
testisUBERON:000047396.12gold quality
left uterine tubeUBERON:000130396.06gold quality
body of uterusUBERON:000985395.96gold quality
left lobe of thyroid glandUBERON:000112095.95gold quality
thyroid glandUBERON:000204695.95gold quality
right lobe of thyroid glandUBERON:000111995.91gold quality
ectocervixUBERON:001224995.89gold quality
adenohypophysisUBERON:000219695.79gold quality
body of pancreasUBERON:000115095.74gold quality
pituitary glandUBERON:000000795.72gold quality
uterine cervixUBERON:000000295.55gold quality
myometriumUBERON:000129695.47gold quality
gall bladderUBERON:000211095.28gold quality
upper lobe of left lungUBERON:000895295.24gold quality
mucosa of stomachUBERON:000119995.20gold quality
placentaUBERON:000198795.19gold quality
right lungUBERON:000216795.17gold quality
pancreasUBERON:000126495.05gold quality
fallopian tubeUBERON:000388995.05gold quality
right uterine tubeUBERON:000130294.83gold quality
descending thoracic aortaUBERON:000234594.82gold quality
prostate glandUBERON:000236794.79gold quality
vaginaUBERON:000099694.78gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.17
E-GEOD-75367no40.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR

miRNA regulators (miRDB)

127 targeting GNL1, 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-126-5P100.0072.713180
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4481100.0066.421669
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-806899.9873.852376
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-652-5P99.9167.49505
HSA-MIR-129799.9173.413162
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-95-5P99.8972.173973
HSA-MIR-629-3P99.8567.991875
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-489-3P99.8066.46839
HSA-MIR-4694-3P99.7969.532640
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-62399.7668.161170
HSA-MIR-2116-3P99.7464.32889
HSA-MIR-149-3P99.7268.223963

Literature-anchored findings (GeneRIF, showing 4)

  • The results demonstrated that multiple mechanisms are involved in the translocation of GNL1 to the nucleolus in a cell cycle-dependent manner to regulate cell growth and proliferation. (PMID:22244851)
  • The results suggested that SNPs at PRR3 and ABCF1 genes and the haplotype composed by SNPs at GNL1 and PRR3 between the HLA-A and HLA-C genes tended to predict Graves ophthalmology in a gender-dependent manner in patients with Graves Disease in Taiwan. (PMID:24908204)
  • cross-talk between GNL1 and RPS20 is critical to promote cell proliferation. (PMID:30061673)
  • Guanine nucleotide binding protein like-1 (GNL1) promotes cancer cell proliferation and survival through AKT/p21 (CIP1) signaling cascade. (PMID:33147101)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriognl1ENSDARG00000061789
mus_musculusGnl1ENSMUSG00000024429
rattus_norvegicusGnl1ENSRNOG00000000798
drosophila_melanogasterNs4FBGN0032882

Paralogs (6): LSG1 (ENSG00000041802), NOA1 (ENSG00000084092), GNL3L (ENSG00000130119), GNL2 (ENSG00000134697), MTG1 (ENSG00000148824), GNL3 (ENSG00000163938)

Protein

Protein identifiers

Guanine nucleotide-binding protein-like 1P36915 (reviewed: P36915)

Alternative names: GTP-binding protein HSR1

All UniProt accessions (3): A0A024RCR2, A2AB27, P36915

UniProt curated annotations — full annotation on UniProt →

Function. Possible regulatory or functional link with the histocompatibility cluster.

Domain organisation. In contrast to other GTP-binding proteins, this family is characterized by a circular permutation of the GTPase motifs described by a G4-G1-G3 pattern.

Similarity. Belongs to the TRAFAC class YlqF/YawG GTPase family.

Isoforms (2)

UniProt IDNamesCanonical?
P36915-11yes
P36915-22

RefSeq proteins (1): NP_005266* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006073GTP-bdDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR030378G_CP_domDomain
IPR043358GNL1-likeFamily

Pfam: PF01926

UniProt features (27 total): modified residue 11, sequence conflict 4, compositionally biased region 3, binding site 3, region of interest 2, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P36915-F177.410.53

Functional residue map

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

Ligand- & substrate-binding residues (3): 225–228; 367–374; 411–415

Post-translational modifications (11): 32, 33, 34, 48, 50, 51, 68, 324, 561, 562, 563

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 153 (showing top): ATF_B, CMYB_01, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, CREBP1_Q2, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, CREB_Q4, GOBP_LYMPHOCYTE_MEDIATED_IMMUNITY, E4F1_Q6, GOBP_DNA_DAMAGE_RESPONSE, GOBP_ADAPTIVE_IMMUNE_RESPONSE, ATF3_Q6, CREB_Q2_01

GO Biological Process (3): T cell mediated immunity (GO:0002456), DNA damage response (GO:0006974), signal transduction (GO:0007165)

GO Molecular Function (4): GTPase activity (GO:0003924), structural molecule activity (GO:0005198), GTP binding (GO:0005525), nucleotide binding (GO:0000166)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lymphocyte mediated immunity1
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains1
cellular response to stress1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
ribonucleoside triphosphate phosphatase activity1
molecular_function1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2485 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GNL1EEF1A1P04719970
GNL1HSF1Q00613839
GNL1EEF1A2P54266713
GNL1HLA-EP13747620
GNL1MITD1Q8WV92540
GNL1PPP1R11O60927532
GNL1BOP1Q14137532
GNL1C6orf136Q5SQH8519
GNL1TCF19Q9Y242508
GNL1GTPBP4Q9BZE4481
GNL1ABCF1Q8NE71476
GNL1SMCHD1A6NHR9469
GNL1HLA-CP04222464
GNL1XPO1O14980455
GNL1PRKNO60260454

IntAct

54 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
DYNC1I2DYNC1LI2psi-mi:“MI:0914”(association)0.680
SLC2A12METTL15psi-mi:“MI:0914”(association)0.530
KLHL40CBX4psi-mi:“MI:0914”(association)0.530
WDCPPAPSS1psi-mi:“MI:0914”(association)0.530
ABCF2AHCYL1psi-mi:“MI:0914”(association)0.530
GNL1CSNK2A2psi-mi:“MI:0914”(association)0.530
GNL1FAUpsi-mi:“MI:0915”(physical association)0.400
GNL1HINT1psi-mi:“MI:0915”(physical association)0.400
FGBNME2psi-mi:“MI:0914”(association)0.350
TULP3PPP1R12Apsi-mi:“MI:0914”(association)0.350
DYNC1I2DYNC1LI2psi-mi:“MI:0914”(association)0.350
CCDC116PAPSS1psi-mi:“MI:0914”(association)0.350
PAPSS1PAPSS2psi-mi:“MI:0914”(association)0.350
CSNK2A1RPS3Apsi-mi:“MI:0914”(association)0.350
CSNK2A2VWA8psi-mi:“MI:0914”(association)0.350
CSNK2BOSBPL8psi-mi:“MI:0914”(association)0.350
PGK1PRPF6psi-mi:“MI:0914”(association)0.350
RACK1RPS3Apsi-mi:“MI:0914”(association)0.350
RPL19RPS3Apsi-mi:“MI:0914”(association)0.350
RPL4EIF3CLpsi-mi:“MI:0914”(association)0.350
SRP14EIF3Fpsi-mi:“MI:0914”(association)0.350
FGBKIF2Apsi-mi:“MI:0914”(association)0.350
PAPSS1ASMTLpsi-mi:“MI:0914”(association)0.350

BioGRID (114): GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Co-fractionation), GNL1 (Affinity Capture-MS)

ESM2 similar proteins: A2VD13, A4D126, A5PK43, A6H751, A7E3N7, B0S6U7, B0S8I0, B5DFG1, D2GU20, E1BCH6, O75127, O75616, O95382, P36915, P36916, P48760, Q05932, Q2TBP8, Q2VPK5, Q3SZK4, Q3U269, Q3U5Q7, Q3V300, Q4R8D2, Q5E9Z1, Q5EBA0, Q5ND52, Q5QJC3, Q5R655, Q5RA07, Q5RJG7, Q5S6T3, Q5TM59, Q6MG06, Q7YR35, Q8C2E4, Q8CJ00, Q8JIF5, Q8K045, Q8NC60

Diamond homologs: A2XGQ1, A4SDB8, A5GR60, A5IMB8, A5N2K5, A5VWQ6, A6LT31, A8EXG4, A8GM60, A8GQS1, A8GUK6, A9KFU3, A9NDV6, B0JFL6, B0KG04, B1JFJ3, B1LBK5, B1X0B0, B2TPB6, B2UX10, B3EGV8, B3PN57, B3QQY9, B3WE42, B4S596, B6J7Q3, B7K1S0, B8GAY7, B8I8N7, B9K8C0, C3PMD9, C4K1B9, J9VQ03, O14236, O67679, O74791, P0CS94, P36915, P36916, P40010

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 63 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Formation of a pool of free 40S subunits511.4×2e-03
L13a-mediated translational silencing of Ceruloplasmin expression510.3×2e-03
SRP-dependent cotranslational protein targeting to membrane510.2×2e-03
GTP hydrolysis and joining of the 60S ribosomal subunit510.2×2e-03
mRNA Splicing - Major Pathway66.7×4e-03
Translation56.3×9e-03

GO biological processes:

GO termPartnersFoldFDR
negative regulation of proteasomal ubiquitin-dependent protein catabolic process534.0×1e-04
cytoplasmic translation618.8×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance57
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1809 predictions. Top by Δscore:

VariantEffectΔscore
6:30546692:TGACC:Tdonor_loss1.0000
6:30546695:CCTTT:Cdonor_gain1.0000
6:30546711:AG:Adonor_gain1.0000
6:30546832:CCAGG:Cacceptor_gain1.0000
6:30546833:CAGG:Cacceptor_gain1.0000
6:30546833:CAGGC:Cacceptor_gain1.0000
6:30546834:AGG:Aacceptor_gain1.0000
6:30546835:GG:Gacceptor_gain1.0000
6:30546837:C:CCacceptor_gain1.0000
6:30547108:TCAC:Tdonor_loss1.0000
6:30547111:C:CAdonor_loss1.0000
6:30547271:GAAC:Gacceptor_gain1.0000
6:30547272:AAC:Aacceptor_gain1.0000
6:30547273:AC:Aacceptor_gain1.0000
6:30547274:CC:Cacceptor_gain1.0000
6:30547275:C:CCacceptor_gain1.0000
6:30552662:C:CCacceptor_gain1.0000
6:30553180:C:CCacceptor_gain1.0000
6:30553187:C:CTacceptor_gain1.0000
6:30553188:A:Tacceptor_gain1.0000
6:30553349:CCA:Cdonor_gain1.0000
6:30553443:T:TAdonor_gain1.0000
6:30554566:AGTAC:Adonor_loss1.0000
6:30554567:GTACT:Gdonor_loss1.0000
6:30554568:TAC:Tdonor_loss1.0000
6:30554569:ACT:Adonor_loss1.0000
6:30554570:CTC:Cdonor_loss1.0000
6:30554571:TC:Tdonor_loss1.0000
6:30554572:CA:Cdonor_loss1.0000
6:30554573:A:ACdonor_gain1.0000

AlphaMissense

3920 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:30547116:A:CC479W1.000
6:30547117:C:TC479Y1.000
6:30554631:A:GW182R1.000
6:30554631:A:TW182R1.000
6:30554643:A:GW178R1.000
6:30554643:A:TW178R1.000
6:30546773:G:TA502D0.999
6:30546776:G:TA501E0.999
6:30546778:T:AR500S0.999
6:30546778:T:GR500S0.999
6:30546779:C:AR500I0.999
6:30546779:C:GR500T0.999
6:30546789:C:GD497H0.999
6:30546831:C:GA483P0.999
6:30547118:A:GC479R0.999
6:30547390:C:GG414R0.999
6:30547394:G:CC412W0.999
6:30547397:G:CD411E0.999
6:30547397:G:TD411E0.999
6:30547398:T:AD411V0.999
6:30547398:T:CD411G0.999
6:30547398:T:GD411A0.999
6:30547452:C:TG393D0.999
6:30547453:C:GG393R0.999
6:30547512:T:AK373M0.999
6:30547515:C:TG372E0.999
6:30553446:A:GW238R0.999
6:30553446:A:TW238R0.999
6:30553480:C:AK226N0.999
6:30553480:C:GK226N0.999

dbSNP variants (sampled 300 via entrez): RS1001394831 (6:30558297 A>G), RS1001406535 (6:30551937 A>T), RS1001418217 (6:30544101 G>A), RS1001476892 (6:30543792 C>T), RS1002401263 (6:30544412 C>A,G,T), RS1002778126 (6:30544135 T>C), RS1002809569 (6:30554593 G>A), RS1003065219 (6:30548130 T>C), RS1003388554 (6:30553317 C>A,T), RS1003475422 (6:30557932 A>G), RS1003755192 (6:30549881 T>C,G), RS1003764487 (6:30542553 G>T), RS1003809864 (6:30546441 A>T), RS1003818499 (6:30542122 C>G,T), RS1003872791 (6:30545417 C>T)

Disease associations

OMIM: gene MIM:143024 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

22 associations (top):

StudyTraitp-value
GCST004521_114Autism spectrum disorder or schizophrenia3.000000e-17
GCST004521_117Autism spectrum disorder or schizophrenia3.000000e-15
GCST004521_121Autism spectrum disorder or schizophrenia3.000000e-13
GCST004521_132Autism spectrum disorder or schizophrenia2.000000e-09
GCST004521_171Autism spectrum disorder or schizophrenia4.000000e-14
GCST004521_2Autism spectrum disorder or schizophrenia2.000000e-16
GCST004521_209Autism spectrum disorder or schizophrenia5.000000e-16
GCST004521_210Autism spectrum disorder or schizophrenia5.000000e-15
GCST004521_211Autism spectrum disorder or schizophrenia5.000000e-15
GCST004521_263Autism spectrum disorder or schizophrenia7.000000e-17
GCST004521_265Autism spectrum disorder or schizophrenia7.000000e-14
GCST004521_269Autism spectrum disorder or schizophrenia7.000000e-11
GCST004521_295Autism spectrum disorder or schizophrenia6.000000e-18
GCST004521_3Autism spectrum disorder or schizophrenia2.000000e-15
GCST004521_56Autism spectrum disorder or schizophrenia1.000000e-22
GCST004521_70Autism spectrum disorder or schizophrenia8.000000e-20
GCST004521_79Autism spectrum disorder or schizophrenia1.000000e-16
GCST004748_102Lung cancer2.000000e-18
GCST004750_52Squamous cell lung carcinoma5.000000e-14
GCST005232_23Neuroticism8.000000e-09
GCST005790_55Rosacea symptom severity2.000000e-06
GCST006041_32Major depressive disorder1.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007660neuroticism measurement
EFO:0009180rosacea severity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Benzo(a)pyreneaffects methylation, decreases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
bisphenol Fincreases methylation1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
decabromobiphenyl etherdecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteincreases expression1
tetrabromobisphenol Adecreases expression1
zinc chromatedecreases expression, increases abundance1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent ionincreases abundance, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
LDN 193189affects cotreatment, increases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects methylation1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Ozoneaffects expression, increases abundance1
Phthalic Acidsincreases methylation1
Quercetinincreases phosphorylation1
Ribonucleotidesaffects binding1
Seleniumincreases expression1
Smokedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.