LTV1

gene
On this page

Also known as FLJ14909dJ468K18.4

Summary

LTV1 (LTV1 ribosome biogenesis factor, HGNC:21173) is a protein-coding gene on chromosome 6q24.2, encoding Protein LTV1 homolog (Q96GA3). Essential for ribosome biogenesis. It is a selective cancer dependency (DepMap: 89.9% of cell lines).

Predicted to be involved in ribosomal small subunit biogenesis and ribosomal small subunit export from nucleus. Located in cytosol and nucleoplasm. Implicated in inflammatory poikiloderma with hair abnormalities and acral keratoses.

Source: NCBI Gene 84946 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): inflammatory poikiloderma with hair abnormalities and acral keratoses (Moderate, GenCC)
  • Clinical variants (ClinVar): 78 total — 1 pathogenic
  • Phenotypes (HPO): 11
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 89.9% of screened cell lines
  • MANE Select transcript: NM_032860

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21173
Approved symbolLTV1
NameLTV1 ribosome biogenesis factor
Location6q24.2
Locus typegene with protein product
StatusApproved
AliasesFLJ14909, dJ468K18.4
Ensembl geneENSG00000135521
Ensembl biotypeprotein_coding
OMIM620074
Entrez84946

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000367576, ENST00000868801, ENST00000918498, ENST00000918499, ENST00000918500, ENST00000918501, ENST00000970779

RefSeq mRNA: 2 — MANE Select: NM_032860 NM_001329953, NM_032860

CCDS: CCDS5201

Canonical transcript exons

ENST00000367576 — 11 exons

ExonStartEnd
ENSE00000455901143862104143862243
ENSE00000764889143850131143850218
ENSE00000764892143860426143860553
ENSE00000764894143862844143862896
ENSE00000764895143863086143863286
ENSE00000799013143846051143846224
ENSE00001122515143857752143858007
ENSE00001122520143857303143857444
ENSE00001445066143863417143863812
ENSE00001445069143843338143843480
ENSE00003508857143844486143844617

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 95.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 38.5626 / max 486.0804, expressed in 1820 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
7026837.56381818
702670.9988631

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
epithelial cell of pancreasCL:000008395.82gold quality
left ventricle myocardiumUBERON:000656691.50silver quality
gastrocnemiusUBERON:000138891.41gold quality
upper arm skinUBERON:000426391.19gold quality
kidney epitheliumUBERON:000481991.09silver quality
monocyteCL:000057690.99gold quality
skin of abdomenUBERON:000141690.97gold quality
cardiac muscle of right atriumUBERON:000337990.86silver quality
muscle of legUBERON:000138390.77gold quality
leukocyteCL:000073890.62gold quality
left uterine tubeUBERON:000130390.45gold quality
oocyteCL:000002390.25gold quality
spermCL:000001990.23gold quality
smooth muscle tissueUBERON:000113590.16gold quality
body of pancreasUBERON:000115090.16gold quality
skin of legUBERON:000151189.95gold quality
myocardiumUBERON:000234989.93silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.87gold quality
peritoneumUBERON:000235889.75gold quality
omental fat padUBERON:001041489.75gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.59gold quality
zone of skinUBERON:000001489.55gold quality
deltoidUBERON:000147689.49gold quality
left adrenal glandUBERON:000123489.45gold quality
right adrenal gland cortexUBERON:003582789.44gold quality
islet of LangerhansUBERON:000000689.41gold quality
pancreasUBERON:000126489.39gold quality
vermiform appendixUBERON:000115489.30gold quality
adipose tissue of abdominal regionUBERON:000780889.28gold quality
left adrenal gland cortexUBERON:003582589.25gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.59
E-MTAB-7249no312.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting LTV1, 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-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5692A100.0074.406850
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-338-5P99.9272.342951
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-369-3P99.8570.522264
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-447099.6669.351767
HSA-MIR-545-5P99.6670.182308
HSA-MIR-5197-5P99.6469.081494
HSA-MIR-432899.5771.064094
HSA-MIR-392399.5269.21446
HSA-MIR-21-5P99.4670.541035
HSA-MIR-16-2-3P99.2970.601954

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 89.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head. (PMID:30348748)
  • Mutations in the ribosome biogenesis factor gene LTV1 are linked to LIPHAK syndrome, a novel poikiloderma-like disorder. (PMID:34999892)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioltv1ENSDARG00000008490
mus_musculusLtv1ENSMUSG00000019814
rattus_norvegicusLtv1ENSRNOG00000015217
drosophila_melanogasterLTV1FBGN0027525
caenorhabditis_elegansT23D8.3WBGENE00011944

Protein

Protein identifiers

Protein LTV1 homologQ96GA3 (reviewed: Q96GA3)

All UniProt accessions (1): Q96GA3

UniProt curated annotations — full annotation on UniProt →

Function. Essential for ribosome biogenesis.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in the epidermis.

Disease relevance. Inflammatory poikiloderma with hair abnormalities and acral keratoses (IPHAK) [MIM:620199] An autosomal recessive disorder characterized by mottled hyper- and hypopigmentation of the skin, sparse scalp hair and eyelashes, sparse or absent eyebrows, and palmoplantar keratoses. The disease may be caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the LTV1 family.

RefSeq proteins (2): NP_001316882, NP_116249* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007307Ltv1Family

Pfam: PF04180

UniProt features (22 total): modified residue 5, region of interest 4, helix 4, strand 3, compositionally biased region 2, chain 1, sequence variant 1, turn 1, coiled-coil region 1

Structure

Experimental structures (PDB)

13 structures.

PDBMethodResolution (Å)
7WTUELECTRON MICROSCOPY3
7WTZELECTRON MICROSCOPY3
7WTTELECTRON MICROSCOPY3.1
7WTXELECTRON MICROSCOPY3.1
7WTWELECTRON MICROSCOPY3.2
7WU0ELECTRON MICROSCOPY3.3
6G18ELECTRON MICROSCOPY3.6
8ZDDELECTRON MICROSCOPY3.7
8ZDCELECTRON MICROSCOPY3.8
6G4SELECTRON MICROSCOPY4
6G51ELECTRON MICROSCOPY4.1
6G4WELECTRON MICROSCOPY4.5
6G53ELECTRON MICROSCOPY4.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96GA3-F169.240.09

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 (5): 248, 331, 408, 17, 24

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72312rRNA processing
R-HSA-8868773rRNA processing in the nucleus and cytosol
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 164 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_NUCLEAR_TRANSPORT, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_NUCLEAR_EXPORT, MODULE_207, GOBP_ORGANELLE_LOCALIZATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, GOCC_PRERIBOSOME, GOCC_RIBONUCLEOPROTEIN_COMPLEX, SCGGAAGY_ELK1_02, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, GOBP_RIBOSOMAL_SMALL_SUBUNIT_EXPORT_FROM_NUCLEUS

GO Biological Process (3): ribosomal small subunit export from nucleus (GO:0000056), ribosome biogenesis (GO:0042254), ribosomal small subunit biogenesis (GO:0042274)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), preribosome, small subunit precursor (GO:0030688), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
rRNA processing in the nucleus and cytosol1
Metabolism of RNA1
rRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
ribonucleoprotein complex biogenesis2
ribosomal subunit export from nucleus1
ribosome biogenesis1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1
preribosome1
intracellular anatomical structure1

Protein interactions and networks

STRING

2668 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LTV1BYSLQ13895991
LTV1RIOK2Q9BVS4943
LTV1TSR1Q2NL82943
LTV1PNO1Q9NRX1916
LTV1RRAGCQ9HB90894
LTV1NOB1Q9ULX3889
LTV1RPS3P23396838
LTV1XPO1O14980823
LTV1RRP12Q5JTH9795
LTV1RPS10P46783779
LTV1RIOK1Q9BRS2776
LTV1NMD3Q96D46725
LTV1RPS20P17075690
LTV1TXNL4BQ9NX01678
LTV1GPATCH2Q9NW75637

IntAct

182 interactions, top by confidence:

ABTypeScore
BMI1CBX4psi-mi:“MI:0914”(association)0.900
BYSLLTV1psi-mi:“MI:0915”(physical association)0.870
LTV1BYSLpsi-mi:“MI:0915”(physical association)0.870
PCGF2CBX4psi-mi:“MI:0914”(association)0.840
RPS3LTV1psi-mi:“MI:0915”(physical association)0.800
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
BYSLPARNpsi-mi:“MI:0914”(association)0.640
TSR1RPS3psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
RACK1RIOK3psi-mi:“MI:0914”(association)0.640
LTV1CSNK2A1psi-mi:“MI:0217”(phosphorylation reaction)0.590
GAS2L2LTV1psi-mi:“MI:0915”(physical association)0.560
RPS14MAGEB2psi-mi:“MI:0914”(association)0.560
ZNF324BZNF316psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
ZBTB48ZBTB24psi-mi:“MI:0914”(association)0.530
TSR1PARNpsi-mi:“MI:0914”(association)0.530
CBX6IGF2BP3psi-mi:“MI:0914”(association)0.530
RIOK2BYSLpsi-mi:“MI:0914”(association)0.530
RPS3ZNF316psi-mi:“MI:0914”(association)0.530

BioGRID (260): LTV1 (Two-hybrid), LTV1 (Affinity Capture-MS), LTV1 (Affinity Capture-MS), LTV1 (Affinity Capture-MS), LTV1 (Affinity Capture-MS), LTV1 (Affinity Capture-MS), LTV1 (Co-fractionation), LTV1 (Affinity Capture-MS), LTV1 (Reconstituted Complex), LTV1 (Proximity Label-MS), LTV1 (Proximity Label-MS), LTV1 (Proximity Label-MS), LTV1 (Proximity Label-MS), LTV1 (Proximity Label-MS), LTV1 (Proximity Label-MS)

ESM2 similar proteins: A4IGY3, A7SD85, A9ULY7, B0W6N3, C8VBH3, O08837, O57476, P0CO94, P0CO95, P39964, P51951, P92948, Q0VC06, Q13435, Q16543, Q173M7, Q28HX4, Q2KJC1, Q3TQI7, Q3UJB0, Q4P652, Q4R6Y7, Q4V838, Q4WHG0, Q4WVH3, Q51LS1, Q52G60, Q5EAC6, Q5H7N8, Q5R8B2, Q5RC87, Q5ZKI4, Q5ZKM1, Q61081, Q63692, Q6A068, Q6AYJ5, Q6DD06, Q7JWR9, Q7K3D8

Diamond homologs: Q0VC06, Q4V838, Q5R8B2, Q5U3J8, Q68FR7, Q6NSQ7, Q7KN79, Q8T1D4, Q96GA3, Q10191

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 188 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
Eukaryotic Translation Initiation1433.5×1e-16
Cap-dependent Translation Initiation1433.5×1e-16
SARS-CoV-1 modulates host translation machinery1433.5×1e-16
Eukaryotic Translation Elongation1430.2×3e-16
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S1429.5×4e-16
Nonsense-Mediated Decay (NMD)1527.1×2e-16
Influenza Viral RNA Transcription and Replication1525.1×4e-16
SARS-CoV-2 modulates host translation machinery1424.3×6e-15

GO biological processes:

GO termPartnersFoldFDR
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)728.4×7e-07
maturation of SSU-rRNA627.7×9e-06
cytoplasmic translation1921.2×3e-17
ribosomal small subunit biogenesis1520.6×2e-13
stress granule assembly518.1×6e-04
mRNA stabilization613.2×5e-04
translation2012.4×9e-14
negative regulation of proteasomal ubiquitin-dependent protein catabolic process512.1×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance58
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2443758NM_032860.5(LTV1):c.503A>G (p.Asn168Ser)Pathogenic

SpliceAI

2203 predictions. Top by Δscore:

VariantEffectΔscore
6:143844577:A:Gdonor_gain1.0000
6:143844618:G:GGdonor_gain1.0000
6:143846049:A:AGacceptor_gain1.0000
6:143846050:G:GGacceptor_gain1.0000
6:143846050:GATA:Gacceptor_gain1.0000
6:143846192:A:Tdonor_gain1.0000
6:143846224:AGTAA:Adonor_loss1.0000
6:143846225:G:GGdonor_gain1.0000
6:143846225:GT:Gdonor_loss1.0000
6:143846226:T:Gdonor_loss1.0000
6:143850128:A:AGacceptor_gain1.0000
6:143850129:A:Gacceptor_gain1.0000
6:143850130:GA:Gacceptor_gain1.0000
6:143857297:TTCTA:Tacceptor_loss1.0000
6:143857298:TCTA:Tacceptor_loss1.0000
6:143857299:CTA:Cacceptor_loss1.0000
6:143857301:A:ACacceptor_loss1.0000
6:143857301:A:AGacceptor_gain1.0000
6:143857301:AG:Aacceptor_gain1.0000
6:143857302:G:GTacceptor_gain1.0000
6:143857302:GG:Gacceptor_gain1.0000
6:143857386:G:GTdonor_gain1.0000
6:143857404:GCCAA:Gdonor_gain1.0000
6:143857421:A:Tdonor_gain1.0000
6:143857425:G:GTdonor_gain1.0000
6:143857432:G:Tdonor_gain1.0000
6:143857445:G:GGdonor_gain1.0000
6:143858004:GAAG:Gdonor_gain1.0000
6:143858006:AGGTA:Adonor_loss1.0000
6:143858007:GGT:Gdonor_loss1.0000

AlphaMissense

3173 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:143844534:T:CF18L0.998
6:143844536:T:AF18L0.998
6:143844536:T:GF18L0.998
6:143844535:T:CF18S0.997
6:143844549:C:GR23G0.997
6:143844550:G:CR23P0.997
6:143844562:A:GD27G0.996
6:143844598:T:AV39D0.996
6:143844601:T:CL40P0.996
6:143844601:T:AL40Q0.995
6:143846130:T:CL72P0.995
6:143850147:T:CL109S0.995
6:143857338:G:CA145P0.995
6:143844561:G:CD27H0.994
6:143857342:T:CL146P0.994
6:143863421:G:CR441P0.994
6:143844552:A:CS24R0.993
6:143844554:C:AS24R0.993
6:143844554:C:GS24R0.993
6:143844563:T:AD27E0.993
6:143844563:T:GD27E0.993
6:143857335:G:CA144P0.993
6:143844544:T:AV21D0.992
6:143844562:A:CD27A0.992
6:143844562:A:TD27V0.992
6:143862234:T:CS352P0.992
6:143863282:G:CR438P0.992
6:143844559:G:CR26P0.991
6:143850195:T:CL125S0.991
6:143862243:A:CS355R0.990

dbSNP variants (sampled 300 via entrez): RS1000147197 (6:143843943 T>G), RS1000175575 (6:143847849 CT>C,CTT), RS1000298555 (6:143847607 T>C,G), RS1000365730 (6:143849507 T>C), RS1000450271 (6:143842021 C>G), RS1000498357 (6:143842947 A>T), RS1000501873 (6:143842661 G>A,C), RS1000637476 (6:143853741 C>A,G,T), RS1000757631 (6:143859895 G>A), RS1000813219 (6:143848489 C>T), RS1000852959 (6:143854720 G>C), RS1001037633 (6:143861233 T>C,G), RS1001141294 (6:143860997 G>C), RS1001202373 (6:143857038 G>A,T), RS1001357334 (6:143851007 T>G)

Disease associations

OMIM: gene MIM:620074 | disease phenotypes: MIM:620199

GenCC curated gene-disease

DiseaseClassificationInheritance
inflammatory poikiloderma with hair abnormalities and acral keratosesModerateAutosomal recessive

Mondo (1): inflammatory poikiloderma with hair abnormalities and acral keratoses (MONDO:0859355)

Orphanet (0):

HPO phenotypes

11 total (11 of 11 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000653Sparse eyelashes
HP:0001029Poikiloderma
HP:0001070Mottled pigmentation
HP:0002209Sparse scalp hair
HP:0002223Absent eyebrow
HP:0003593Infantile onset
HP:0011463Childhood onset
HP:0034572Pigment incontinence
HP:0045075Sparse eyebrow
HP:0200016Acrokeratosis

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4742314 (PROTEIN-PROTEIN INTERACTION)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression3
bisphenol Aaffects expression, affects cotreatment, increases methylation2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
dicrotophosdecreases expression1
pirinixic acidaffects binding, increases activity, increases expression1
glycidyl methacrylateincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
coumarinaffects phosphorylation1
cyclic 3’,5’-uridine monophosphateaffects binding1
CGP 52608affects binding, increases reaction1
(+)-JQ1 compounddecreases expression1
Irinotecandecreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Caffeineaffects phosphorylation1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Estradiolincreases expression1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Hydrogen Peroxideaffects expression1
Leadaffects expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Methyl Methanesulfonatedecreases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4713767BindingProtac activity at CRBN/LTV1 in human BxPC-3 cells assessed as LTV1 degradation incubated for 16 hrs by proteomic analysisDiscovery of a Napabucasin PROTAC as an Effective Degrader of the E3 Ligase ZFP91. — J Med Chem

Clinical trials (associated diseases)

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