HNRNPLL

gene
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Summary

HNRNPLL (heterogeneous nuclear ribonucleoprotein L like, HGNC:25127) is a protein-coding gene on chromosome 2p22.1, encoding Heterogeneous nuclear ribonucleoprotein L-like (Q8WVV9). RNA-binding protein that functions as a regulator of alternative splicing for multiple target mRNAs, including PTPRC/CD45 and STAT5A.

HNRNPLL is a master regulator of activation-induced alternative splicing in T cells. In particular, it alters splicing of CD45 (PTPRC; MIM 151460), a tyrosine phosphatase essential for T-cell development and activation (Oberdoerffer et al., 2008 [PubMed 18669861]).

Source: NCBI Gene 92906 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 60 total
  • Druggable target: yes
  • MANE Select transcript: NM_138394

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25127
Approved symbolHNRNPLL
Nameheterogeneous nuclear ribonucleoprotein L like
Location2p22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000143889
Ensembl biotypeprotein_coding
OMIM611208
Entrez92906

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000272249, ENST00000358367, ENST00000378915, ENST00000409328, ENST00000409636, ENST00000410076, ENST00000425682, ENST00000441689, ENST00000449105, ENST00000488099, ENST00000498516, ENST00000608859

RefSeq mRNA: 2 — MANE Select: NM_138394 NM_001142650, NM_138394

CCDS: CCDS1796, CCDS46261

Canonical transcript exons

ENST00000449105 — 13 exons

ExonStartEnd
ENSE000009624853859153038591648
ENSE000012105683858191338581985
ENSE000012105723858564438585881
ENSE000015863133858207238582168
ENSE000018609933860243838602928
ENSE000034951263856838638568443
ENSE000035506373856913338569334
ENSE000035530283856819938568297
ENSE000035894303857746138577532
ENSE000036487083857321038573427
ENSE000036827553856980438569925
ENSE000036872113858384138583926
ENSE000038442623856196938564237

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 96.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.5046 / max 1041.2367, expressed in 1814 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
2788111.83321787
278806.52271670
278832.1880675
278821.1715767
278790.9724581
278780.4161198
278770.2792105
278840.121641

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305396.77gold quality
embryoUBERON:000092296.64gold quality
ganglionic eminenceUBERON:000402396.64gold quality
adrenal tissueUBERON:001830394.73gold quality
adult organismUBERON:000702394.66gold quality
epithelial cell of pancreasCL:000008394.54gold quality
cartilage tissueUBERON:000241893.68gold quality
cortical plateUBERON:000534393.56gold quality
parotid glandUBERON:000183193.12gold quality
cauda epididymisUBERON:000436092.79gold quality
left testisUBERON:000453392.74gold quality
right testisUBERON:000453492.58gold quality
saphenous veinUBERON:000731892.43gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099192.29gold quality
bone marrowUBERON:000237192.19gold quality
smooth muscle tissueUBERON:000113592.09gold quality
testisUBERON:000047391.98gold quality
right uterine tubeUBERON:000130291.95gold quality
endothelial cellCL:000011591.94gold quality
popliteal arteryUBERON:000225091.78gold quality
tibial arteryUBERON:000761091.77gold quality
lower esophagus muscularis layerUBERON:003583391.60gold quality
lower esophagusUBERON:001347391.56gold quality
body of uterusUBERON:000985391.54gold quality
arteryUBERON:000163791.50gold quality
esophagogastric junction muscularis propriaUBERON:003584191.44gold quality
mucosa of stomachUBERON:000119991.43gold quality
bronchial epithelial cellCL:000232891.38gold quality
right lungUBERON:000216791.31gold quality
aortaUBERON:000094791.29gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting HNRNPLL, 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-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-3134100.0066.43777
HSA-MIR-3646100.0073.565283
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-480399.9871.993117
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-570-3P99.9672.414910
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-365899.9673.874379
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-430799.8270.453374
HSA-MIR-4760-5P99.8069.881619
HSA-MIR-451799.7669.191867
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-5580-3P99.7069.412052
HSA-MIR-361899.6968.571012
HSA-MIR-379-3P99.6969.601524
HSA-MIR-411-3P99.6969.631524
HSA-MIR-10393-5P99.6568.011368
HSA-MIR-806199.6369.441411
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-4708-3P99.5167.99870
HSA-MIR-513C-5P99.5068.421730

Literature-anchored findings (GeneRIF, showing 7)

  • Participation of SRRF (Stromal RNA Regulating Factor) isoforms in post-transcriptional events in bone marrow stromal cells; an important role in regulation of the RNA expression that directs the bone marrow stromal cells differentiation pathway (PMID:15256261)
  • identification of heterogeneous ribonucleoprotein L-like (hnRNPLL) as a critical inducible regulator of CD45 alternative splicing (PMID:18669861)
  • These data establish that hnRNP LL plays a critical and unique role in the signal-induced regulation of CD45 and demonstrate the utility of cell-based screens for the identification of novel splicing regulatory factors. (PMID:18719244)
  • Loss-of-function mutation of hnRNPLL disrupts peripheral T cell accumulation even in the absence of CD45 protein, indicating that hnRNPLL acts through an independent mechanism to promote peripheral T cell longevity. (PMID:20505149)
  • The findings demonstrate that the hnRNP L and LL proteins differentially control gene expression programs at multiple levels in the production of two physiologically important hormones. (PMID:29610151)
  • intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation (PMID:29769310)
  • MYB mediates downregulation of the colorectal cancer metastasis suppressor heterogeneous nuclear ribonucleoprotein L-like during epithelial-mesenchymal transition. (PMID:34286904)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioENSDARG00000116101
mus_musculusHnrnpllENSMUSG00000024095
rattus_norvegicusHnrnpllENSRNOG00000006929
drosophila_melanogastersmFBGN0003435
caenorhabditis_elegansWBGENE00016624

Paralogs (5): PTBP1 (ENSG00000011304), HNRNPL (ENSG00000104824), PTBP2 (ENSG00000117569), PTBP3 (ENSG00000119314), RBM20 (ENSG00000203867)

Protein

Protein identifiers

Heterogeneous nuclear ribonucleoprotein L-likeQ8WVV9 (reviewed: Q8WVV9)

Alternative names: Stromal RNA-regulating factor

All UniProt accessions (8): Q8WVV9, A0A0S2Z6K1, B7WPG3, C9IYN3, C9JJZ7, H7BXH8, H7C464, V9GYK2

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein that functions as a regulator of alternative splicing for multiple target mRNAs, including PTPRC/CD45 and STAT5A. Required for alternative splicing of PTPRC.

Subunit / interactions. Interacts with HNRNPL.

Tissue specificity. Widely expressed. Detected in bone marrow stroma cells, skeletal muscle, heart, placenta, pancreas, kidney and lung.

Induction. Up-regulated in stimulated T-cells.

Isoforms (5)

UniProt IDNamesCanonical?
Q8WVV9-11yes
Q8WVV9-22
Q8WVV9-33
Q8WVV9-44
Q8WVV9-55

RefSeq proteins (2): NP_001136122, NP_612403* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR006536HnRNP-L/PTBFamily
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR021790PTBP1-like_RRM2Domain
IPR034983hnRPLL_RRM3Domain
IPR034985hnRPLL_RRM1Domain
IPR034986hnRPLL_RRM2Domain
IPR034987hnRPLL_RRM4Domain
IPR035979RBD_domain_sfHomologous_superfamily
IPR055204HNRNPL_RRMDomain

Pfam: PF00076, PF11835, PF13893, PF22976

UniProt features (28 total): splice variant 6, modified residue 5, strand 5, domain 3, cross-link 2, helix 2, compositionally biased region 2, chain 1, turn 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
7EVSX-RAY DIFFRACTION1.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WVV9-F176.110.49

Functional residue map

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

Post-translational modifications (7): 68, 75, 26, 491, 35, 46, 59

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 217 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, CCAWYNNGAAR_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_RNA_SPLICING, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, BOYLAN_MULTIPLE_MYELOMA_D_DN, MODULE_331, YU_MYC_TARGETS_UP, MARTINEZ_RB1_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOBP_RNA_SPLICING, OCT1_06, MARSON_FOXP3_TARGETS_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, NRF2_01, ZHANG_BREAST_CANCER_PROGENITORS_UP

GO Biological Process (3): mRNA processing (GO:0006397), positive regulation of RNA splicing (GO:0033120), regulation of RNA splicing (GO:0043484)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA binding (GO:0003729), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), membrane (GO:0016020), synapse (GO:0045202), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA splicing2
binding2
RNA processing1
mRNA metabolic process1
positive regulation of gene expression1
regulation of RNA splicing1
regulation of gene expression1
regulation of primary metabolic process1
nucleic acid binding1
RNA binding1
intracellular membrane-bounded organelle1
cellular anatomical structure1
cell junction1
protein-containing complex1

Protein interactions and networks

STRING

994 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HNRNPLLPTPRCP08575799
HNRNPLLHNRNPH1P31943612
HNRNPLLPCBP2Q15366610
HNRNPLLTP53P04637582
HNRNPLLHNRNPCP07910565
HNRNPLLSRSF3P23152564
HNRNPLLHNRNPUQ00839561
HNRNPLLSRSF5Q13243560
HNRNPLLSRSF4Q08170553
HNRNPLLSRSF6Q13247547
HNRNPLLU2AF2P26368546
HNRNPLLSRSF7Q16629545
HNRNPLLSRSF2Q01130531
HNRNPLLHNRNPDLO14979523
HNRNPLLRRM2P31350507

IntAct

120 interactions, top by confidence:

ABTypeScore
HNRNPLLHNRNPKpsi-mi:“MI:0915”(physical association)0.720
HNRNPKHNRNPLLpsi-mi:“MI:0915”(physical association)0.720
HNRNPLLHNRNPKpsi-mi:“MI:0915”(physical association)0.670
HNRNPKHNRNPLLpsi-mi:“MI:0915”(physical association)0.670
BOLLHNRNPLLpsi-mi:“MI:0915”(physical association)0.670
QKIHNRNPLLpsi-mi:“MI:0915”(physical association)0.670
MDFIHNRNPLLpsi-mi:“MI:0915”(physical association)0.670
HNRNPLLBOLLpsi-mi:“MI:0915”(physical association)0.670
HNRNPLLQKIpsi-mi:“MI:0915”(physical association)0.670
HNRNPLLMDFIpsi-mi:“MI:0915”(physical association)0.670
DAB1HNRNPLLpsi-mi:“MI:0915”(physical association)0.560
UBE2IHNRNPLLpsi-mi:“MI:0915”(physical association)0.560
RBPMSHNRNPLLpsi-mi:“MI:0915”(physical association)0.560
RHOXF2HNRNPLLpsi-mi:“MI:0915”(physical association)0.560
HNRNPLLTHAP1psi-mi:“MI:0915”(physical association)0.560
HNRNPLLDAB1psi-mi:“MI:0915”(physical association)0.560

BioGRID (229): HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Two-hybrid), HNRNPLL (Affinity Capture-MS), HNRNPLL (Affinity Capture-MS), HNRNPLL (Affinity Capture-MS), HNRNPLL (Affinity Capture-MS), CCNB2 (Co-fractionation)

ESM2 similar proteins: A1L1G1, A7MBL8, A8KBF6, B2RYD2, O00560, O08874, O08992, O60733, O94806, P10687, P10894, P29074, P70175, P97570, Q16513, Q28C55, Q3SYX0, Q3US41, Q4R4Q3, Q5PYH7, Q5R8R4, Q5ZLR4, Q62433, Q62936, Q640Z1, Q69YN2, Q6DCD0, Q6DEZ7, Q6DFS4, Q6DIX1, Q6GQL1, Q6JE36, Q6NXG1, Q6P0D7, Q6R005, Q7ZVR8, Q7ZY29, Q8BPM2, Q8BWW9, Q8K0G8

Diamond homologs: F1LQ48, P14866, Q8R081, Q8WVV9, Q921F4, Q9FGL9, Q9MAC5, O95758, P17225, P26599, Q00438, Q29099, Q66H20, Q6ICX4, Q8BHD7, Q8WN55, Q91Z31, Q9UKA9, Q9Z118, E9PT37, P0DW16, P25299, Q3UQS8, Q5T481

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 109 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
mRNA Polyadenylation79.2×5e-03
Processing of Capped Intron-Containing Pre-mRNA78.6×5e-03
mRNA Splicing - Major Pathway86.5×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance47
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2511 predictions. Top by Δscore:

VariantEffectΔscore
2:38568193:A:ACdonor_gain1.0000
2:38568194:C:CCdonor_gain1.0000
2:38568194:CTTA:Cdonor_gain1.0000
2:38568195:TTAC:Tdonor_loss1.0000
2:38568196:TACTC:Tdonor_loss1.0000
2:38568197:A:ACdonor_gain1.0000
2:38568197:A:Cdonor_loss1.0000
2:38568197:ACT:Adonor_gain1.0000
2:38568198:C:CAdonor_gain1.0000
2:38568198:CT:Cdonor_gain1.0000
2:38568198:CTC:Cdonor_gain1.0000
2:38568198:CTCG:Cdonor_gain1.0000
2:38568198:CTCGG:Cdonor_gain1.0000
2:38568211:T:Cdonor_gain1.0000
2:38568293:TGAAG:Tacceptor_gain1.0000
2:38568294:GAAG:Gacceptor_gain1.0000
2:38568295:AAG:Aacceptor_gain1.0000
2:38568296:AG:Aacceptor_gain1.0000
2:38568298:C:CCacceptor_gain1.0000
2:38568304:C:CTacceptor_gain1.0000
2:38568305:A:Tacceptor_gain1.0000
2:38568379:CACTT:Cdonor_loss1.0000
2:38568380:ACTT:Adonor_loss1.0000
2:38568381:CT:Cdonor_loss1.0000
2:38568382:TTAC:Tdonor_loss1.0000
2:38568383:TACG:Tdonor_loss1.0000
2:38568384:A:ACdonor_gain1.0000
2:38568384:ACGTT:Adonor_loss1.0000
2:38568385:C:Adonor_loss1.0000
2:38568385:C:CCdonor_gain1.0000

AlphaMissense

3534 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:38564201:G:AS537F1.000
2:38564203:A:CF536L1.000
2:38564203:A:TF536L1.000
2:38564204:A:GF536S1.000
2:38564205:A:GF536L1.000
2:38564206:G:CC535W1.000
2:38564207:C:TC535Y1.000
2:38564208:A:GC535R1.000
2:38564210:A:GL534P1.000
2:38564210:A:TL534H1.000
2:38564212:C:AK533N1.000
2:38564212:C:GK533N1.000
2:38564214:T:CK533E1.000
2:38568219:T:GH518P1.000
2:38568221:A:CN517K1.000
2:38568221:A:TN517K1.000
2:38568225:A:GL516P1.000
2:38568234:A:GL513P1.000
2:38568234:A:TL513H1.000
2:38568246:G:TA509E1.000
2:38568265:A:GW503R1.000
2:38568265:A:TW503R1.000
2:38568273:A:GL500P1.000
2:38568276:C:AG499V1.000
2:38568276:C:TG499E1.000
2:38568277:C:AG499W1.000
2:38568277:C:GG499R1.000
2:38568277:C:TG499R1.000
2:38568396:A:CF488L1.000
2:38568396:A:TF488L1.000

dbSNP variants (sampled 300 via entrez): RS1000005261 (2:38561575 A>C,T), RS1000120394 (2:38564020 G>A,C,T), RS1000137908 (2:38597754 T>A), RS1000246726 (2:38566942 G>C), RS1000295617 (2:38579448 T>A), RS1000361751 (2:38589037 A>G), RS1000426814 (2:38597473 G>A,C), RS1000440656 (2:38572874 C>T), RS1000471628 (2:38573073 T>C), RS1000528602 (2:38583316 A>G), RS1000602270 (2:38577951 C>G,T), RS1000615800 (2:38578692 C>G), RS1000668811 (2:38579166 G>A), RS1000720691 (2:38593483 G>A), RS1000808322 (2:38571694 T>A)

Disease associations

OMIM: gene MIM:611208 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST004904_222Body mass index9.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724650 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, decreases methylation4
trichostatin Aaffects cotreatment, decreases expression3
sodium arsenitedecreases expression, increases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression2
FR900359affects phosphorylation1
urushiolincreases expression1
ethylbenzeneincreases expression1
beta-lapachonedecreases expression1
perfluorooctanoic acidincreases expression1
2-xyleneincreases expression1
coumarinaffects phosphorylation1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1
jinfukangdecreases expression1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1
Bortezomibincreases expression1
Benzeneincreases expression1
Cadmiumincreases abundance, increases expression1
Caffeinedecreases phosphorylation1
Endosulfandecreases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Ivermectindecreases expression1
Methylene Chlorideincreases expression1
Oxazoloneincreases expression1
Phthalic Acidsincreases methylation1
Quercetindecreases phosphorylation1
Ribonucleotidesaffects binding1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651577BindingBinding affinity to human HNRNPLL incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E0ECUbigene HeLa HNRNPLL KOCancer cell lineFemale

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.