LUC7L

gene
On this page

Also known as LUC7B1hLuc7B1Luc7

Summary

LUC7L (LUC7 like, HGNC:6723) is a protein-coding gene on chromosome 16p13.3, encoding Putative RNA-binding protein Luc7-like 1 (Q9NQ29). May bind to RNA via its Arg/Ser-rich domain.

The LUC7L gene may represent a mammalian heterochromatic gene, encoding a putative RNA-binding protein similar to the yeast Luc7p subunit of the U1 snRNP splicing complex that is normally required for 5-prime splice site selection (Tufarelli et al., 2001 [PubMed 11170747]).

Source: NCBI Gene 55692 — RefSeq curated summary.

At a glance

  • GWAS associations: 28
  • Clinical variants (ClinVar): 72 total — 1 pathogenic
  • MANE Select transcript: NM_201412

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6723
Approved symbolLUC7L
NameLUC7 like
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesLUC7B1, hLuc7B1, Luc7
Ensembl geneENSG00000007392
Ensembl biotypeprotein_coding
OMIM607782
Entrez55692

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 19 protein_coding, 7 retained_intron, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000293872, ENST00000337351, ENST00000397780, ENST00000397783, ENST00000418978, ENST00000419516, ENST00000426094, ENST00000428363, ENST00000429378, ENST00000430864, ENST00000442701, ENST00000443357, ENST00000464711, ENST00000467552, ENST00000468732, ENST00000469109, ENST00000490762, ENST00000494366, ENST00000494545, ENST00000495349, ENST00000629543, ENST00000862883, ENST00000862884, ENST00000920887, ENST00000920888, ENST00000920889, ENST00000920890, ENST00000920891, ENST00000949701, ENST00000949702

RefSeq mRNA: 4 — MANE Select: NM_201412 NM_001320226, NM_001330420, NM_018032, NM_201412

CCDS: CCDS10401, CCDS32348, CCDS81921

Canonical transcript exons

ENST00000293872 — 10 exons

ExonStartEnd
ENSE00003464528188990189339
ENSE00003469522199062199238
ENSE00003527983208078208188
ENSE00003529172192927193015
ENSE00003602151189968190135
ENSE00003643311220649220747
ENSE00003681185227242227336
ENSE00003784923190541190570
ENSE00003787006206004206147
ENSE00003902541229279229449

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 98.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 52.2463 / max 380.4320, expressed in 1822 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
15571150.27281822
1557101.1053640
2076850.8682551

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818898.92gold quality
sural nerveUBERON:001548898.43gold quality
adenohypophysisUBERON:000219698.35gold quality
left lobe of thyroid glandUBERON:000112098.25gold quality
right lobe of thyroid glandUBERON:000111998.14gold quality
cerebellar hemisphereUBERON:000224597.90gold quality
pituitary glandUBERON:000000797.89gold quality
right uterine tubeUBERON:000130297.88gold quality
right hemisphere of cerebellumUBERON:001489097.88gold quality
lower esophagus mucosaUBERON:003583497.77gold quality
cerebellar cortexUBERON:000212997.76gold quality
thyroid glandUBERON:000204697.69gold quality
endocervixUBERON:000045897.66gold quality
body of uterusUBERON:000985397.54gold quality
left ovaryUBERON:000211997.43gold quality
right ovaryUBERON:000211897.41gold quality
body of pancreasUBERON:000115097.32gold quality
right frontal lobeUBERON:000281097.12gold quality
granulocyteCL:000009496.95gold quality
metanephros cortexUBERON:001053396.91gold quality
cerebellumUBERON:000203796.90gold quality
muscle layer of sigmoid colonUBERON:003580596.88gold quality
ganglionic eminenceUBERON:000402396.87gold quality
cortical plateUBERON:000534396.86gold quality
anterior cingulate cortexUBERON:000983596.72gold quality
cingulate cortexUBERON:000302796.69gold quality
adrenal tissueUBERON:001830396.69gold quality
left uterine tubeUBERON:000130396.64gold quality
small intestine Peyer’s patchUBERON:000345496.55gold quality
C1 segment of cervical spinal cordUBERON:000646996.54gold 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

Upstream regulators (CollecTRI, top): E2F4

miRNA regulators (miRDB)

17 targeting LUC7L, 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-590-3P99.9674.346478
HSA-MIR-545-3P99.9570.742783
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-806799.8669.592260
HSA-MIR-128399.6972.423009
HSA-MIR-7844-5P99.5568.561428
HSA-MIR-519D-5P99.4169.302057
HSA-MIR-429199.2068.882969
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-770299.0665.95698
HSA-MIR-361-5P98.9570.161340
HSA-MIR-4711-5P98.8968.00965
HSA-MIR-374A-3P98.8767.821531
HSA-MIR-10395-3P98.1066.701726
HSA-MIR-506-5P98.0267.411065
HSA-MIR-151A-3P95.5265.29516
HSA-MIR-1247-3P83.6963.1899

Literature-anchored findings (GeneRIF, showing 1)

  • Functional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms. (PMID:33852859)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioluc7lENSDARG00000055903
mus_musculusLuc7lENSMUSG00000024188
rattus_norvegicusLuc7lENSRNOG00000020488
drosophila_melanogasterCG7564FBGN0036734
caenorhabditis_elegansWBGENE00015207

Paralogs (2): LUC7L3 (ENSG00000108848), LUC7L2 (ENSG00000146963)

Protein

Protein identifiers

Putative RNA-binding protein Luc7-like 1Q9NQ29 (reviewed: Q9NQ29)

Alternative names: Putative SR protein LUC7B1, SR+89

All UniProt accessions (10): Q9NQ29, A8MYV2, B8ZZ08, B8ZZ09, B8ZZ10, B8ZZ12, F2Z322, F8WBC1, H7C2U4, Q1W6G4

UniProt curated annotations — full annotation on UniProt →

Function. May bind to RNA via its Arg/Ser-rich domain.

Tissue specificity. Ubiquitous.

Miscellaneous. May be due to an intron retention.

Similarity. Belongs to the Luc7 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9NQ29-11yes
Q9NQ29-22
Q9NQ29-33

RefSeq proteins (4): NP_001307155, NP_001317349, NP_060502, NP_958815* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004882Luc7-relFamily

Pfam: PF03194

UniProt features (14 total): compositionally biased region 4, modified residue 3, splice variant 2, coiled-coil region 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NQ29-F168.180.08

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): 363, 332, 336

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 200 (showing top): RRAGTTGT_UNKNOWN, AP1_01, GOBP_MUSCLE_TISSUE_DEVELOPMENT, HNF3ALPHA_Q6, TTTGTAG_MIR520D, RACCACAR_AML_Q6, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, EVI1_05, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, MYOD_01, AML_Q6, BACH2_01, WTGAAAT_UNKNOWN

GO Biological Process (4): mRNA splice site recognition (GO:0006376), negative regulation of striated muscle tissue development (GO:0045843), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (4): mRNA binding (GO:0003729), identical protein binding (GO:0042802), RS domain binding (GO:0050733), protein binding (GO:0005515)

GO Cellular Component (3): U1 snRNP (GO:0005685), U2-type prespliceosome (GO:0071004), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
spliceosomal complex assembly1
protein-RNA complex assembly1
striated muscle tissue development1
regulation of striated muscle tissue development1
negative regulation of muscle organ development1
negative regulation of muscle tissue development1
mRNA metabolic process1
RNA binding1
protein binding1
protein domain specific binding1
binding1
spliceosomal snRNP complex1
U2-type spliceosomal complex1
U1 snRNP1
U2 snRNP1
prespliceosome1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1282 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LUC7LRBM25P49756982
LUC7LSNRNP70P08621924
LUC7LRBM39Q14498890
LUC7LPRPF40AO75400888
LUC7LSNRPCP09234880
LUC7LHBQ1P09105856
LUC7LRSRC1Q96IZ7855
LUC7LSRSF5Q13243761
LUC7LSNRPAP09012747
LUC7LHBA1P01922740
LUC7LU2AF1Q01081698
LUC7LNCBP2P52298653
LUC7LPRPF39Q86UA1622
LUC7LSF3B3Q15393619
LUC7LSRSF1Q07955604

IntAct

122 interactions, top by confidence:

ABTypeScore
EAF1ELL2psi-mi:“MI:0914”(association)0.840
SRPK2LUC7Lpsi-mi:“MI:0217”(phosphorylation reaction)0.780
CSNK2BRPS6KA5psi-mi:“MI:0914”(association)0.660
CHCHD10CLPXpsi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
LUC7LSRPK1psi-mi:“MI:0217”(phosphorylation reaction)0.640
ZRANB2PIP4K2Apsi-mi:“MI:0914”(association)0.610
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
LUC7LSPRED1psi-mi:“MI:0915”(physical association)0.560
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
LUC7L2ZNF593psi-mi:“MI:0914”(association)0.530
CHERPLUC7Lpsi-mi:“MI:0915”(physical association)0.510
LUC7LLUC7Lpsi-mi:“MI:0915”(physical association)0.510
RNASEH1LUC7Lpsi-mi:“MI:0915”(physical association)0.500
LUC7LTSC1psi-mi:“MI:0915”(physical association)0.370
LUC7LPRDX1psi-mi:“MI:0915”(physical association)0.370
TCERG1LUC7Lpsi-mi:“MI:0915”(physical association)0.370
GADD45GLUC7Lpsi-mi:“MI:0915”(physical association)0.370
CTNNBL1LUC7Lpsi-mi:“MI:0915”(physical association)0.370
LUC7LPRMT5psi-mi:“MI:0915”(physical association)0.370
Dynlrb1DYNC1LI2psi-mi:“MI:0914”(association)0.350
C1qbppsi-mi:“MI:0914”(association)0.350
NLRP3PHRF1psi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350

BioGRID (400): LUC7L (Affinity Capture-MS), LUC7L (Affinity Capture-MS), LUC7L (Affinity Capture-MS), LUC7L (Affinity Capture-MS), LUC7L (Affinity Capture-MS), LUC7L2 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM26 (Affinity Capture-MS), ZFP91 (Affinity Capture-MS), MRPL46 (Affinity Capture-MS), EIF2B1 (Affinity Capture-MS), ZC3H18 (Affinity Capture-MS), NKAP (Affinity Capture-MS), BCLAF1 (Affinity Capture-MS), THRAP3 (Affinity Capture-MS)

ESM2 similar proteins: A2AQ19, B2GV05, O54941, O55047, O95232, P08621, P09406, P23588, P50502, P52756, P97762, Q07866, Q08CW1, Q13123, Q1ECX4, Q1RMR2, Q1RMU5, Q32KT0, Q3SX41, Q56A18, Q5NVI3, Q5R8W6, Q5RAD5, Q5RF31, Q5SRX1, Q5SUF2, Q5U2T8, Q5U2U0, Q5ZI03, Q62376, Q66HG8, Q66II8, Q6PH81, Q7TNC4, Q86UE8, Q86X95, Q8BGD9, Q8C0V0, Q8TA86, Q90ZY6

Diamond homologs: O95232, Q07508, Q3SX41, Q54XQ8, Q5R8W6, Q5SUF2, Q7TNC4, Q9CYI4, Q9NQ29, Q9USM4, Q9VVI1, Q9Y383, Q09217

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 147 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
Transport of Mature Transcript to Cytoplasm518.7×1e-04
RNA Polymerase II Transcription Termination817.2×4e-07
mRNA 3’-end processing815.4×1e-06
Nonsense-Mediated Decay (NMD)613.7×1e-04
Peptide chain elongation1113.7×4e-08
Viral mRNA Translation1113.7×4e-08
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1113.5×4e-08
Selenocysteine synthesis1113.0×4e-08

GO biological processes:

GO termPartnersFoldFDR
negative regulation of mRNA splicing, via spliceosome634.8×4e-06
cytoplasmic translation1216.8×5e-09
ribosomal small subunit biogenesis712.1×3e-04
RNA processing711.6×3e-04
regulation of alternative mRNA splicing, via spliceosome611.1×1e-03
translation1310.1×2e-07
RNA splicing128.0×7e-06
mRNA splicing, via spliceosome106.9×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance53
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
15680NC_000016.10:g.174045_192395delPathogenic

SpliceAI

2065 predictions. Top by Δscore:

VariantEffectΔscore
16:189929:A:ACdonor_gain1.0000
16:189929:ACT:Adonor_gain1.0000
16:189930:C:CCdonor_gain1.0000
16:189930:CTC:Cdonor_gain1.0000
16:189966:A:ACdonor_gain1.0000
16:189967:C:CCdonor_gain1.0000
16:192925:ACCT:Adonor_gain1.0000
16:192926:CCTC:Cdonor_gain1.0000
16:192928:T:TAdonor_gain1.0000
16:193013:TTT:Tacceptor_gain1.0000
16:199056:ACAT:Adonor_loss1.0000
16:199057:CATA:Cdonor_loss1.0000
16:199060:A:Tdonor_loss1.0000
16:199060:AC:Adonor_gain1.0000
16:199061:C:Tdonor_loss1.0000
16:199061:CC:Cdonor_gain1.0000
16:199067:A:Cdonor_gain1.0000
16:199111:TTGC:Tdonor_gain1.0000
16:199112:TGCC:Tdonor_gain1.0000
16:199235:CTTC:Cacceptor_gain1.0000
16:199236:TTC:Tacceptor_gain1.0000
16:199238:CCT:Cacceptor_loss1.0000
16:199239:C:CAacceptor_loss1.0000
16:199239:C:CCacceptor_gain1.0000
16:205994:T:Cdonor_gain1.0000
16:206041:T:TAdonor_gain1.0000
16:206144:CTGC:Cacceptor_gain1.0000
16:206147:CCT:Cacceptor_loss1.0000
16:206148:C:CCacceptor_gain1.0000
16:206148:CTGTG:Cacceptor_loss1.0000

AlphaMissense

2417 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:199075:A:GL225P1.000
16:199084:C:GR222P1.000
16:199085:G:CR222G1.000
16:199095:G:CF218L1.000
16:199095:G:TF218L1.000
16:199096:A:GF218S1.000
16:199097:A:GF218L1.000
16:199099:C:TG217E1.000
16:199100:C:AG217W1.000
16:199100:C:GG217R1.000
16:199100:C:TG217R1.000
16:199104:G:CH215Q1.000
16:199104:G:TH215Q1.000
16:199105:T:CH215R1.000
16:199106:G:CH215D1.000
16:199106:G:TH215N1.000
16:199108:A:GL214S1.000
16:199110:C:AK213N1.000
16:199110:C:GK213N1.000
16:199112:T:CK213E1.000
16:199114:C:AG212V1.000
16:199114:C:GG212A1.000
16:199114:C:TG212D1.000
16:199115:C:AG212C1.000
16:199115:C:GG212R1.000
16:199115:C:TG212S1.000
16:199117:C:TG211D1.000
16:199119:G:CF210L1.000
16:199119:G:TF210L1.000
16:199120:A:CF210C1.000

dbSNP variants (sampled 300 via entrez): RS1000034731 (16:218416 G>T), RS1000191719 (16:200967 A>G), RS1000292110 (16:214091 G>GC), RS1000320242 (16:215584 T>C), RS1000344083 (16:208030 G>C), RS1000379162 (16:223272 CAG>C), RS1000379851 (16:210741 G>A), RS1000395119 (16:205908 A>T), RS1000576118 (16:215083 CTTTT>C,CTT,CTTT,CTTTTT), RS1000616026 (16:229092 C>A,G,T), RS1000691185 (16:229259 G>A,C,T), RS1000692070 (16:196135 C>T), RS1000729919 (16:209532 A>G), RS1000838907 (16:204491 G>A), RS1000856362 (16:215217 A>G)

Disease associations

OMIM: gene MIM:607782 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

28 associations (top):

StudyTraitp-value
GCST000587_1Mean corpuscular hemoglobin3.000000e-09
GCST004334_13Mean corpuscular hemoglobin5.000000e-07
GCST004602_221Mean corpuscular volume4.000000e-38
GCST004605_11Mean corpuscular hemoglobin concentration2.000000e-11
GCST004615_103Hemoglobin concentration7.000000e-12
GCST004615_104Hemoglobin concentration4.000000e-10
GCST004621_82Red cell distribution width3.000000e-14
GCST004630_170Mean corpuscular hemoglobin6.000000e-68
GCST006804_150Red cell distribution width2.000000e-10
GCST006979_944Heel bone mineral density8.000000e-10
GCST90002385_68High light scatter reticulocyte count3.000000e-14
GCST90002385_69High light scatter reticulocyte count4.000000e-16
GCST90002386_277High light scatter reticulocyte percentage of red cells1.000000e-15
GCST90002390_631Mean corpuscular hemoglobin1.000000e-65
GCST90002390_632Mean corpuscular hemoglobin6.000000e-31
GCST90002391_162Mean corpuscular hemoglobin concentration3.000000e-39
GCST90002391_163Mean corpuscular hemoglobin concentration8.000000e-30
GCST90002391_164Mean corpuscular hemoglobin concentration1.000000e-09
GCST90002392_478Mean corpuscular volume9.000000e-53
GCST90002392_479Mean corpuscular volume2.000000e-26
GCST90002396_646Mean reticulocyte volume4.000000e-40
GCST90002397_274Mean spheric corpuscular volume3.000000e-24
GCST90002403_658Red blood cell count9.000000e-20
GCST90002403_659Red blood cell count3.000000e-11
GCST90002404_330Red cell distribution width1.000000e-34
GCST90002405_352Reticulocyte count4.000000e-21
GCST90002405_353Reticulocyte count4.000000e-14
GCST90002406_428Reticulocyte fraction of red cells2.000000e-13

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004509hemoglobin measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0009188Red cell distribution width
EFO:0009270heel bone mineral density
EFO:0007986reticulocyte count
EFO:0010701mean reticulocyte volume
EFO:0004305erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression6
bisphenol Aaffects cotreatment, increases methylation, increases expression, decreases reaction, increases abundance3
sodium arsenitedecreases expression2
Hydrogen Peroxideincreases expression, affects expression2
Tobacco Smoke Pollutiondecreases expression, decreases methylation2
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, decreases expression1
ginger extractincreases expression, decreases reaction, increases abundance1
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
deoxynivalenolincreases expression1
beta-lapachonedecreases expression, increases expression1
aflatoxin B2increases methylation1
coumarinincreases phosphorylation1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
avobenzoneincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Saffects cotreatment, decreases expression1
PCI 5002affects cotreatment, increases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
Bortezomibincreases expression1
Resveratrolincreases expression, affects cotreatment1
Temozolomideincreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Vorinostatdecreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsincreases oxidation, affects cotreatment, increases abundance1
Benzo(a)pyreneaffects methylation1

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.