LARP6

gene
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Also known as acheronFLJ11196

Summary

LARP6 (La ribonucleoprotein 6, translational regulator, HGNC:24012) is a protein-coding gene on chromosome 15q23, encoding La-related protein 6 (Q9BRS8). Regulates the coordinated translation of type I collagen alpha-1 and alpha-2 mRNAs, CO1A1 and CO1A2.

Enables RNA binding activity and myosin binding activity. Involved in positive regulation of collagen biosynthetic process. Located in cytoplasm and nucleus.

Source: NCBI Gene 55323 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 81 total
  • Druggable target: yes
  • MANE Select transcript: NM_018357

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24012
Approved symbolLARP6
NameLa ribonucleoprotein 6, translational regulator
Location15q23
Locus typegene with protein product
StatusApproved
Aliasesacheron, FLJ11196
Ensembl geneENSG00000166173
Ensembl biotypeprotein_coding
OMIM611300
Entrez55323

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000299213, ENST00000344870, ENST00000559140, ENST00000559316, ENST00000560052

RefSeq mRNA: 2 — MANE Select: NM_018357 NM_018357, NM_197958

CCDS: CCDS10236, CCDS32281

Canonical transcript exons

ENST00000299213 — 3 exons

ExonStartEnd
ENSE000011005117085388970854157
ENSE000011225847082913070833116
ENSE000035206497083629570836505

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 98.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 68.1071 / max 600.0407, expressed in 1474 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
15073859.63241474
1507376.38261292
1507361.4889774
1507390.5107303
1507350.05075
1507340.04184

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lateral globus pallidusUBERON:000247698.11gold quality
inferior vagus X ganglionUBERON:000536397.66gold quality
mucosa of stomachUBERON:000119997.61gold quality
left testisUBERON:000453397.55gold quality
lateral nuclear group of thalamusUBERON:000273697.33gold quality
right testisUBERON:000453497.25gold quality
C1 segment of cervical spinal cordUBERON:000646997.16gold quality
spinal cordUBERON:000224096.82gold quality
subthalamic nucleusUBERON:000190696.79gold quality
inferior olivary complexUBERON:000212796.56gold quality
dorsal plus ventral thalamusUBERON:000189796.32gold quality
substantia nigra pars reticulataUBERON:000196696.00gold quality
medulla oblongataUBERON:000189695.97gold quality
ponsUBERON:000098895.92gold quality
putamenUBERON:000187495.74gold quality
ventral tegmental areaUBERON:000269195.73gold quality
spermCL:000001995.61gold quality
substantia nigra pars compactaUBERON:000196595.58gold quality
superior vestibular nucleusUBERON:000722795.57gold quality
testisUBERON:000047395.38gold quality
dorsal motor nucleus of vagus nerveUBERON:000287095.25gold quality
midbrainUBERON:000189195.23gold quality
substantia nigraUBERON:000203895.14gold quality
prefrontal cortexUBERON:000045195.13gold quality
stromal cell of endometriumCL:000225595.06gold quality
corpus callosumUBERON:000233694.97gold quality
middle temporal gyrusUBERON:000277194.56gold quality
Ammon’s hornUBERON:000195494.48gold quality
caudate nucleusUBERON:000187394.29gold quality
Brodmann (1909) area 46UBERON:000648394.29gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-9435yes1081.94
E-HCAD-13yes24.99
E-ANND-3yes20.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting LARP6, 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-3924100.0072.092394
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-4455100.0065.481587
HSA-MIR-6772-5P99.9467.01577
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-6715A-3P99.8368.051473
HSA-MIR-60999.8264.26505
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-57799.7869.132479
HSA-MIR-58799.6470.862611
HSA-MIR-751599.3168.221795
HSA-MIR-133A-3P99.2771.531270
HSA-MIR-133B99.2771.531270
HSA-MIR-10399-5P99.1769.872610
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-6715B-3P98.8068.071204
HSA-MIR-876-3P98.7668.23945
HSA-MIR-5197-3P98.7167.051905
HSA-MIR-4704-3P98.2869.331300
HSA-MIR-64397.3567.91805
HSA-MIR-215-3P97.0268.011209
HSA-MIR-6854-5P96.7765.96848
HSA-MIR-426496.3564.761480
HSA-MIR-3677-5P93.1664.62393
HSA-MIR-126-3P91.0764.8722

Literature-anchored findings (GeneRIF, showing 16)

  • These data define Achn as a newly discovered regulatory molecule that presumably mediates a variety of developmental and homeostatic processes in animals. (PMID:17383118)
  • Acheron may influence differentiation in part via its control of cell adhesion dynamics. (PMID:19889961)
  • LARP6 has a distinctive bipartite RNA binding domain not found in other members of the La superfamily. LARP6 interacts with the two single-stranded regions of the 5’ stem-loop. (PMID:19917293)
  • Achn enhances human breast tumor growth and vascularization and that this activity is dependent on nuclear localization. (PMID:21387291)
  • Acheron regulates vascular endothelial proliferation and angiogenesis together with Id1 during wound healing. (PMID:22139627)
  • The results demonstrate that the La modules of the human LARP6 is also active in tRNA-mediated suppression, even in the absence of stable UUU-3’OH trailer protection. (PMID:23887937)
  • LARP6 is a critical mediator by which IGF-1 augments synthesis of collagen type I in vascular smooth muscle (PMID:24469459)
  • We postulate that collagen mRNAs directly partition to the endoplasmic reticulum membrane prior to synthesis of the signal peptide and that LARP6 and nonmuscle myosin filaments mediate this process. (PMID:25271881)
  • The study presents the structure of the La motif and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. (PMID:25488812)
  • Data indicate that LA motif protein LARP6 binding to spliced leader RNA (5’SL) of collagen alpha2(I) mRNA is more stable than the binding to 5’SL of alpha1(I) mRNA. (PMID:25692237)
  • Akt mediated phosphorylation of LARP6; critical step in biosynthesis of type I collagen (PMID:26932461)
  • Study shows that mTORC1 phosphorylates La ribonucleoprotein domain family, member 6 to stimulate type I collagen expression. (PMID:28112218)
  • A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. (PMID:28782243)
  • Characterization of Sequence-Specific Binding of LARP6 to the 5’ Stem-Loop of Type I Collagen mRNAs and Implications for Rational Design of Antifibrotic Drugs. (PMID:34896113)
  • LARP6 Regulates Keloid Fibroblast Proliferation, Invasion, and Ability to Synthesize Collagen. (PMID:35176288)
  • LARP6 suppresses colorectal cancer progression through ZNF267/SGMS2-mediated imbalance of sphingomyelin synthesis. (PMID:36691044)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriolarp6aENSDARG00000005355
mus_musculusLarp6ENSMUSG00000034839
rattus_norvegicusLarp6ENSRNOG00000012438
drosophila_melanogasterLarp4BFBGN0035424
drosophila_melanogasterlarpFBGN0261618
caenorhabditis_eleganslarp-5WBGENE00004147
caenorhabditis_elegansWBGENE00020097

Paralogs (6): LARP4B (ENSG00000107929), SSB (ENSG00000138385), LARP1B (ENSG00000138709), LARP1 (ENSG00000155506), LARP4 (ENSG00000161813), LARP7 (ENSG00000174720)

Protein

Protein identifiers

La-related protein 6Q9BRS8 (reviewed: Q9BRS8)

Alternative names: Acheron, La ribonucleoprotein domain family member 6

All UniProt accessions (3): Q9BRS8, H0YMC6, K7EPD2

UniProt curated annotations — full annotation on UniProt →

Function. Regulates the coordinated translation of type I collagen alpha-1 and alpha-2 mRNAs, CO1A1 and CO1A2. Stabilizes mRNAs through high-affinity binding of a stem-loop structure in their 5’ UTR. This regulation requires VIM and MYH10 filaments, and the helicase DHX9.

Subunit / interactions. Interacts (via the HTH domain) with VIM/vimentin. Interacts (via C-terminus) with non-muscle myosin MYH10. Interacts (via C-terminus) with DHX9.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed in numerous tissues.

Domain organisation. The RRM domain mediates the association with collagen mRNAs stem-loops.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BRS8-11yes
Q9BRS8-22

RefSeq proteins (2): NP_060827, NP_932062 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002344Lupus_LaFamily
IPR006630La_HTHDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR024642SUZ-CDomain
IPR034880LARP6_RRMDomain
IPR035979RBD_domain_sfHomologous_superfamily
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily
IPR045180La_dom_protFamily

Pfam: PF05383, PF12901

UniProt features (44 total): strand 8, helix 8, turn 8, compositionally biased region 5, modified residue 3, domain 3, region of interest 3, short sequence motif 2, initiator methionine 1, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
2MTFSOLUTION NMR
2MTGSOLUTION NMR
9NGXSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BRS8-F161.160.12

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 (3): 2, 56, 58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 109 (showing top): BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, MENSE_HYPOXIA_UP, DITTMER_PTHLH_TARGETS_UP, MODULE_493, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, BASAKI_YBX1_TARGETS_UP, DOUGLAS_BMI1_TARGETS_UP, chr15q23, VECCHI_GASTRIC_CANCER_EARLY_DN, HAN_SATB1_TARGETS_DN, LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP

GO Biological Process (3): RNA processing (GO:0006396), regulation of translation (GO:0006417), positive regulation of collagen biosynthetic process (GO:0032967)

GO Molecular Function (8): mRNA binding (GO:0003729), myosin binding (GO:0017022), RNA stem-loop binding (GO:0035613), mRNA 5’-UTR binding (GO:0048027), sequence-specific mRNA binding (GO:1990825), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA binding2
mRNA binding2
binding2
gene expression1
RNA biosynthetic process1
primary metabolic process1
translation1
post-transcriptional regulation of gene expression1
regulation of protein metabolic process1
positive regulation of biosynthetic process1
positive regulation of collagen metabolic process1
collagen biosynthetic process1
regulation of collagen biosynthetic process1
cytoskeletal protein binding1
nucleic acid binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
protein-containing complex1

Protein interactions and networks

STRING

576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LARP6LARP4BQ92615742
LARP6LARP4Q71RC2725
LARP6STRAPQ9Y3F4618
LARP6DHX9Q08211606
LARP6TM2D3Q9BRN9514
LARP6CSDE1O75534491
LARP6MAB21L3Q8N8X9488
LARP6PABPC1P11940470
LARP6FKBP3Q00688460
LARP6NKX6-3A6NJ46444
LARP6GMNCA6NCL1436
LARP6ODAD4Q96NG3434
LARP6SLC35D3Q5M8T2433
LARP6SLC30A8Q8IWU4424
LARP6LRRC49Q8IUZ0418
LARP6PEX5LQ8IYB4418

IntAct

5 interactions, top by confidence:

ABTypeScore
STRAPCDK2AP1psi-mi:“MI:0914”(association)0.530
STRAPGEMIN2psi-mi:“MI:0914”(association)0.350
ADARB1LARP6psi-mi:“MI:0915”(physical association)0.000

BioGRID (14): LARP6 (Affinity Capture-MS), LARP6 (Protein-RNA), LARP6 (Protein-RNA), LARP6 (Proximity Label-MS), LARP6 (Affinity Capture-MS), LARP6 (Reconstituted Complex), LARP6 (Two-hybrid), ITSN2 (Cross-Linking-MS (XL-MS)), DNAJC11 (Cross-Linking-MS (XL-MS)), DNAJC18 (Cross-Linking-MS (XL-MS)), LARP6 (Cross-Linking-MS (XL-MS)), LARP6 (Cross-Linking-MS (XL-MS)), LARP6 (Two-hybrid), APP (Reconstituted Complex)

ESM2 similar proteins: A0JNJ1, A5PMU4, A6QQV9, A7E3S4, D4AB98, F7EL49, P15056, P34908, P59672, P97306, Q04982, Q13905, Q15678, Q16825, Q5F488, Q5TCQ9, Q5TCZ1, Q62130, Q62136, Q62728, Q6DD51, Q6H8Q1, Q6KC51, Q6P9K8, Q6ZMT1, Q80T23, Q80YS6, Q812E4, Q8BL65, Q8BN59, Q8BZ71, Q8BZI0, Q8N556, Q8R1B0, Q8TDW5, Q8TED9, Q8TEW8, Q8VH46, Q8VHK2, Q8WXD9

Diamond homologs: D5MCN2, J9VT60, O80567, P05455, P10881, P25567, P28048, P28049, P32067, P33399, P38656, P40796, Q05CL8, Q12034, Q26457, Q28G87, Q4G0J3, Q4R627, Q5XI01, Q659C4, Q6PKG0, Q6ZQ58, Q71RC2, Q7ZWE3, Q8BN59, Q8BWW4, Q8RWR2, Q94A38, Q94K80, Q9BRS8, Q9I7T7, Q9LHL3, Q9P6K0, Q9VAW5, P87058, Q04504, Q940X9, Q0V7U7, Q93ZV7, Q6A0A2

SIGNOR signaling

6 interactions.

AEffectBMechanism
LARP6“up-regulates activity”DHX9binding
AKT“up-regulates activity”LARP6phosphorylation
AKT1“up-regulates activity”LARP6phosphorylation
VIM“up-regulates activity”LARP6binding
MTOR“up-regulates activity”LARP6phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance76
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

331 predictions. Top by Δscore:

VariantEffectΔscore
15:70833117:C:CAacceptor_loss1.0000
15:70833118:T:Aacceptor_loss1.0000
15:70836291:TCA:Tdonor_loss1.0000
15:70836292:CACC:Cdonor_loss1.0000
15:70836293:A:ATdonor_loss1.0000
15:70836294:CCTTT:Cdonor_loss1.0000
15:70836501:TGCCA:Tacceptor_gain1.0000
15:70836502:GCCA:Gacceptor_gain1.0000
15:70836503:CCA:Cacceptor_gain1.0000
15:70836503:CCAC:Cacceptor_gain1.0000
15:70836504:CA:Cacceptor_gain1.0000
15:70836504:CAC:Cacceptor_gain1.0000
15:70836505:ACTGA:Aacceptor_loss1.0000
15:70836506:C:CCacceptor_gain1.0000
15:70836506:CTGA:Cacceptor_loss1.0000
15:70836513:C:CTacceptor_gain1.0000
15:70836513:C:Tacceptor_gain1.0000
15:70836514:A:Tacceptor_gain1.0000
15:70833114:CAC:Cacceptor_gain0.9900
15:70833117:C:CCacceptor_gain0.9900
15:70836328:A:Cdonor_gain0.9900
15:70836345:T:TAdonor_gain0.9900
15:70853886:TA:Tdonor_loss0.9900
15:70853888:C:CAdonor_loss0.9900
15:70853991:T:TAdonor_gain0.9900
15:70833113:TCAC:Tacceptor_gain0.9800
15:70833114:CACC:Cacceptor_gain0.9800
15:70833120:C:CTacceptor_gain0.9800
15:70833121:A:Tacceptor_gain0.9800
15:70836293:A:ACdonor_gain0.9800

AlphaMissense

3244 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:70833021:C:AR169S1.000
15:70833021:C:GR169S1.000
15:70833022:C:AR169M1.000
15:70833022:C:GR169T1.000
15:70833055:A:TL158H1.000
15:70833073:A:CL152W1.000
15:70833076:G:TA151D1.000
15:70833095:A:GW145R1.000
15:70833095:A:TW145R1.000
15:70833111:T:AK139N1.000
15:70833111:T:GK139N1.000
15:70833113:T:CK139E1.000
15:70836302:A:GF135S1.000
15:70836311:A:GL132P1.000
15:70836311:A:TL132H1.000
15:70836314:A:GL131P1.000
15:70836314:A:TL131Q1.000
15:70836316:C:AK130N1.000
15:70836316:C:GK130N1.000
15:70836318:T:CK130E1.000
15:70836320:A:TV129D1.000
15:70836322:G:CS128R1.000
15:70836322:G:TS128R1.000
15:70836324:T:GS128R1.000
15:70836326:A:TV127E1.000
15:70836332:C:AG125V1.000
15:70836332:C:TG125E1.000
15:70836333:C:GG125R1.000
15:70836333:C:TG125R1.000
15:70836343:C:AR121S1.000

dbSNP variants (sampled 300 via entrez): RS1000144874 (15:70855394 T>G), RS1000205198 (15:70847955 A>G), RS1000239839 (15:70841014 T>C), RS1000337405 (15:70834048 G>A,C), RS1000390085 (15:70834419 G>A,T), RS1000429168 (15:70837672 T>A), RS1000495710 (15:70855097 G>A), RS1000592140 (15:70840713 A>G), RS1000626345 (15:70843719 G>C), RS1000669889 (15:70849562 A>T), RS1000980316 (15:70846274 T>C), RS1001056340 (15:70855776 G>C), RS1001095592 (15:70852932 G>A), RS1001183905 (15:70830386 A>C), RS1001353056 (15:70847233 T>C)

Disease associations

OMIM: gene MIM:611300 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001212_6Proinsulin levels2.000000e-10
GCST009863_24Insulin-related traits (multivariate analysis)3.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004467insulin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4739702 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression9
Benzo(a)pyreneincreases expression, increases methylation4
Cyclosporineincreases expression4
sodium arsenitedecreases expression, increases expression3
Acetaminophenincreases expression2
Air Pollutantsincreases abundance, increases expression, decreases expression2
Cisplatinaffects expression, decreases expression2
Dexamethasonedecreases expression, affects cotreatment2
Nickeldecreases expression2
Tunicamycinincreases expression2
Particulate Matterincreases abundance, increases expression, decreases expression2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
bisphenol Adecreases methylation1
beta-lapachoneincreases expression1
methylparabenincreases expression1
o,p’-DDTincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chlorideincreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
beta-methylcholineaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001increases expression1
CC-8490increases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, decreases expression1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4689799BindingInhibition of LARP6 La module (unknown origin) binding with collagen 5’ stem loop mRNA at > 2.5 uM by gel mobility shift assayDiscovery of a Lead Compound for Specific Inhibition of Type I Collagen Production in Fibrosis. — ACS Med Chem Lett

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.