LENG1

Summary

LENG1 (leukocyte receptor cluster member 1, HGNC:15502) is a protein-coding gene on chromosome 19q13.42, encoding Leukocyte receptor cluster member 1 (Q96BZ8). It is a selective cancer dependency (DepMap: 27.3% of cell lines).

Predicted to be located in nucleoplasm.

Source: NCBI Gene 79165 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 71 total — 1 likely-pathogenic
• Cancer dependency (DepMap): dependent in 27.3% of screened cell lines
• MANE Select transcript: NM_024316

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15502
Approved symbol	LENG1
Name	leukocyte receptor cluster member 1
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000105617
Ensembl biotype	protein_coding
Entrez	79165

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000222224

RefSeq mRNA: 1 — MANE Select: NM_024316 NM_024316

CCDS: CCDS12881

Canonical transcript exons

ENST00000222224 — 4 exons

Exon	Start	End
ENSE00001051713	54159564	54159721
ENSE00001122492	54156763	54157025
ENSE00001122497	54158282	54158461
ENSE00001122505	54155161	54155940

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 87.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.3965 / max 186.1153, expressed in 1805 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182592	14.2068	1793
182593	5.1897	1721

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	87.57	gold quality
granulocyte	CL:0000094	87.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.24	gold quality
gastrocnemius	UBERON:0001388	84.34	gold quality
apex of heart	UBERON:0002098	84.20	gold quality
muscle of leg	UBERON:0001383	83.89	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.42	gold quality
leukocyte	CL:0000738	83.06	gold quality
monocyte	CL:0000576	83.01	gold quality
mucosa of transverse colon	UBERON:0004991	83.01	gold quality
heart left ventricle	UBERON:0002084	82.77	gold quality
blood	UBERON:0000178	82.70	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	82.21	gold quality
skeletal muscle tissue	UBERON:0001134	81.77	gold quality
calcaneal tendon	UBERON:0003701	81.55	gold quality
popliteal artery	UBERON:0002250	81.38	gold quality
tibial artery	UBERON:0007610	81.37	gold quality
heart	UBERON:0000948	80.90	gold quality
fundus of stomach	UBERON:0001160	80.73	gold quality
thoracic aorta	UBERON:0001515	80.64	gold quality
body of stomach	UBERON:0001161	80.63	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	80.62	gold quality
ascending aorta	UBERON:0001496	80.61	gold quality
left testis	UBERON:0004533	80.41	gold quality
muscle tissue	UBERON:0002385	80.39	gold quality
right adrenal gland	UBERON:0001233	80.36	gold quality
lower esophagus muscularis layer	UBERON:0035833	80.36	gold quality
lower esophagus	UBERON:0013473	80.33	gold quality
right adrenal gland cortex	UBERON:0035827	80.31	gold quality
left coronary artery	UBERON:0001626	80.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.13

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 27.3% of screened cell lines.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	leng1	ENSDARG00000037633
mus_musculus	Leng1	ENSMUSG00000078813
rattus_norvegicus	Leng1	ENSRNOG00000061893
drosophila_melanogaster	CG12818	FBGN0037809
caenorhabditis_elegans	Y18H1A.2	WBGENE00021208

Protein

Protein identifiers

Leukocyte receptor cluster member 1 — Q96BZ8 (reviewed: Q96BZ8)

All UniProt accessions (1): Q96BZ8

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. Belongs to the leukocyte receptor cluster (LRC) present on 19q13.4.

RefSeq proteins (1): NP_077292* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019339	CIR_N_dom	Domain
IPR039875	LENG1-like	Family

Pfam: PF10197

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96BZ8-F1	75.60	0.29

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 (2): 59, 245

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 55 (showing top): BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, REACTOME_MRNA_SPLICING, REACTOME_METABOLISM_OF_RNA, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, ELF2_TARGET_GENES, GREB1_TARGET_GENES, HSD17B8_TARGET_GENES, PRKDC_TARGET_GENES, SALL4_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1768 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LENG1	CNOT3	O75175	617
LENG1	MBOAT7	Q96N66	597
LENG1	CCDC177	Q9NQR7	563
LENG1	RFX8	Q6ZV50	553
LENG1	TFPT	P0C1Z6	504
LENG1	TSEN34	Q9BSV6	490
LENG1	OR14C36	Q8NHC7	476
LENG1	FCAR	P24071	454
LENG1	PRPF31	Q8WWY3	414
LENG1	LENG9	Q96B70	404
LENG1	LILRA5	A6NI73	398
LENG1	C1orf159	Q96HA4	398
LENG1	LAIR1	Q6GTX8	397
LENG1	SLC16A13	Q7RTY0	384
LENG1	PPIL1	Q9Y3C6	376

IntAct

330 interactions, top by confidence:

A	B	Type	Score
GOLGA2	LENG1	psi-mi:“MI:0915”(physical association)	0.790
LENG1	GOLGA2	psi-mi:“MI:0915”(physical association)	0.790
YEATS4	ZNHIT1	psi-mi:“MI:0914”(association)	0.790
LENG1	LDOC1	psi-mi:“MI:0915”(physical association)	0.780
LENG1	CEP70	psi-mi:“MI:0915”(physical association)	0.780
ROPN1	LENG1	psi-mi:“MI:0915”(physical association)	0.780
CEP70	LENG1	psi-mi:“MI:0915”(physical association)	0.780
LENG1	ROPN1	psi-mi:“MI:0915”(physical association)	0.780
LDOC1	LENG1	psi-mi:“MI:0915”(physical association)	0.780
FSD2	LENG1	psi-mi:“MI:0915”(physical association)	0.720
CDR2	LENG1	psi-mi:“MI:0915”(physical association)	0.720
LENG1	KRT31	psi-mi:“MI:0915”(physical association)	0.720
LENG1	NAB2	psi-mi:“MI:0915”(physical association)	0.720
KRT40	LENG1	psi-mi:“MI:0915”(physical association)	0.720
LENG1	TRIM54	psi-mi:“MI:0915”(physical association)	0.720
MID2	LENG1	psi-mi:“MI:0915”(physical association)	0.720
LENG1	FSD2	psi-mi:“MI:0915”(physical association)	0.720
LENG1	CDR2	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (152): LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid), LENG1 (Two-hybrid)

ESM2 similar proteins: A1A5P2, A6QNR1, A8WY26, D3ZND0, O15213, O59678, P27672, P78316, Q0V8M0, Q15050, Q24K12, Q28IV8, Q2KIH4, Q2KII6, Q3T0Q8, Q3T0Z5, Q3UFY0, Q4KLC4, Q5M985, Q5RAS1, Q5RJT2, Q5TAP6, Q5TJE7, Q5ZKM1, Q640M1, Q6EJB6, Q6P0I6, Q6PFJ1, Q8BK35, Q8IY81, Q8N9T8, Q8NEJ9, Q8R3N1, Q8VDQ9, Q96BZ8, Q96EU6, Q9BRP8, Q9BRR8, Q9BVJ6, Q9C086

Diamond homologs: Q3T0Z5, Q96BZ8, Q9DB98

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 86 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.

GO biological processes:

GO term	Partners	Fold	FDR
intermediate filament organization	7	24.4×	7e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	60
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3387818	NM_014516.4(CNOT3):c.2204G>T (p.Arg735Leu)	Likely pathogenic

SpliceAI

483 predictions. Top by Δscore:

Variant	Effect	Δscore
19:54155302:C:CA	acceptor_gain	1.0000
19:54155936:GAGGC:G	acceptor_gain	1.0000
19:54155937:AGGC:A	acceptor_gain	1.0000
19:54155938:GGC:G	acceptor_gain	1.0000
19:54155939:GC:G	acceptor_gain	1.0000
19:54155940:CC:C	acceptor_gain	1.0000
19:54155941:C:CC	acceptor_gain	1.0000
19:54155941:C:T	acceptor_gain	1.0000
19:54155943:G:C	acceptor_gain	1.0000
19:54156761:A:AC	donor_gain	1.0000
19:54156761:ACT:A	donor_gain	1.0000
19:54156762:C:CC	donor_gain	1.0000
19:54156762:CTC:C	donor_gain	1.0000
19:54156764:C:CA	donor_gain	1.0000
19:54156796:T:A	donor_gain	1.0000
19:54158276:GCTTA:G	donor_loss	1.0000
19:54158277:CTTA:C	donor_loss	1.0000
19:54158278:TTACT:T	donor_loss	1.0000
19:54158279:TA:T	donor_loss	1.0000
19:54158280:A:AC	donor_gain	1.0000
19:54158280:ACTT:A	donor_loss	1.0000
19:54158281:C:CG	donor_gain	1.0000
19:54158281:CTTT:C	donor_gain	1.0000
19:54158284:T:A	donor_gain	1.0000
19:54158301:T:TA	donor_gain	1.0000
19:54158340:T:TA	donor_gain	1.0000
19:54158457:CGGGC:C	acceptor_gain	1.0000
19:54158460:GC:G	acceptor_gain	1.0000
19:54158461:CC:C	acceptor_gain	1.0000
19:54158461:CCTGG:C	acceptor_loss	1.0000

AlphaMissense

1685 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:54159669:C:A	W9C	0.998
19:54159669:C:G	W9C	0.998
19:54159671:A:G	W9R	0.998
19:54159671:A:T	W9R	0.998
19:54159688:A:G	I3T	0.998
19:54159666:G:C	H10Q	0.997
19:54159666:G:T	H10Q	0.997
19:54159667:T:C	H10R	0.995
19:54159668:G:C	H10D	0.995
19:54159678:C:A	K6N	0.995
19:54159678:C:G	K6N	0.995
19:54155775:G:C	F247L	0.994
19:54155775:G:T	F247L	0.994
19:54155777:A:G	F247L	0.994
19:54159648:A:C	N16K	0.994
19:54159648:A:T	N16K	0.994
19:54159675:C:A	K7N	0.994
19:54159675:C:G	K7N	0.994
19:54159688:A:C	I3S	0.994
19:54159688:A:T	I3N	0.994
19:54159685:A:G	L4S	0.992
19:54159690:A:C	N2K	0.992
19:54159690:A:T	N2K	0.992
19:54159664:A:T	V11D	0.991
19:54159677:T:C	K7E	0.991
19:54156950:A:G	W130R	0.989
19:54156950:A:T	W130R	0.989
19:54159654:C:A	K14N	0.989
19:54159654:C:G	K14N	0.989
19:54159676:T:A	K7M	0.989

dbSNP variants (sampled 300 via entrez): RS1000142983 (19:54161482 G>A), RS1000201134 (19:54155547 G>A), RS1000332243 (19:54157869 C>G), RS1000427269 (19:54157736 A>T), RS1001246921 (19:54161542 T>G), RS1001784380 (19:54158377 A>G), RS1002216254 (19:54157237 G>A), RS1003143421 (19:54154770 C>T), RS1003220811 (19:54158149 G>A), RS1004127861 (19:54155237 T>G), RS1004243777 (19:54155096 C>G,T), RS1004699546 (19:54159778 C>G,T), RS1005130558 (19:54158417 T>C,G), RS1005251247 (19:54156051 C>A,G), RS1005801458 (19:54160721 C>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:618672

GenCC curated gene-disease

Mondo (1): intellectual developmental disorder with speech delay, autism, and dysmorphic facies (MONDO:0032864)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008758_80	Pre-treatment viral load in HIV-1 infection	2.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010125	viral load

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
ICG 001	decreases expression	1
licochalcone B	increases expression	1
Caffeine	decreases phosphorylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Phenobarbital	affects expression	1
Dronabinol	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Cyclosporine	increases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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