LENG9

Summary

LENG9 (leukocyte receptor cluster member 9, HGNC:16306) is a protein-coding gene on chromosome 19q13.42, encoding Leukocyte receptor cluster member 9 (Q96B70).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 94059 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 134 total
• MANE Select transcript: NM_001301782

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16306
Approved symbol	LENG9
Name	leukocyte receptor cluster member 9
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000275183
Ensembl biotype	protein_coding
Entrez	94059

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000611161

RefSeq mRNA: 1 — MANE Select: NM_001301782 NM_001301782

CCDS: CCDS77358

Canonical transcript exons

ENST00000611161 — 1 exons

Exon	Start	End
ENSE00003720421	54461732	54463778

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 85.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5170 / max 73.8720, expressed in 1582 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182655	3.6323	1466
182654	0.4792	243
182653	0.4055	145

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	85.24	gold quality
mucosa of transverse colon	UBERON:0004991	82.82	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.79	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.52	gold quality
pancreas	UBERON:0001264	77.35	gold quality
duodenum	UBERON:0002114	75.69	gold quality
apex of heart	UBERON:0002098	75.29	gold quality
body of stomach	UBERON:0001161	74.45	gold quality
lower esophagus mucosa	UBERON:0035834	74.22	gold quality
transverse colon	UBERON:0001157	74.16	gold quality
descending thoracic aorta	UBERON:0002345	73.69	gold quality
esophagus mucosa	UBERON:0002469	73.59	gold quality
thoracic aorta	UBERON:0001515	73.38	gold quality
ascending aorta	UBERON:0001496	73.25	gold quality
stromal cell of endometrium	CL:0002255	73.15	gold quality
granulocyte	CL:0000094	73.08	gold quality
minor salivary gland	UBERON:0001830	72.42	gold quality
saliva-secreting gland	UBERON:0001044	72.38	gold quality
prostate gland	UBERON:0002367	72.35	gold quality
stomach	UBERON:0000945	72.10	gold quality
left coronary artery	UBERON:0001626	72.06	gold quality
fundus of stomach	UBERON:0001160	71.70	gold quality
esophagus	UBERON:0001043	71.63	gold quality
left adrenal gland	UBERON:0001234	71.58	gold quality
small intestine	UBERON:0002108	71.49	gold quality
blood	UBERON:0000178	71.48	gold quality
small intestine Peyer’s patch	UBERON:0003454	71.45	gold quality
right coronary artery	UBERON:0001625	71.29	gold quality
right adrenal gland	UBERON:0001233	71.28	gold quality
colon	UBERON:0001155	71.21	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.13

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	leng9	ENSDARG00000062374
mus_musculus	Leng9	ENSMUSG00000043432
rattus_norvegicus	Leng9	ENSRNOG00000069605

Paralogs (1): NUP42 (ENSG00000136243)

Protein

Protein identifiers

Leukocyte receptor cluster member 9 — Q96B70 (reviewed: Q96B70)

All UniProt accessions (1): A0A087WVD1

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_001288711* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR009097	Cyclic_Pdiesterase	Homologous_superfamily
IPR019510	AKAP7-like_phosphoesterase	Domain
IPR040459	MJ1316	Domain
IPR042653	Leng9	Family

Pfam: PF00642, PF04457, PF10469

UniProt features (8 total): region of interest 4, sequence variant 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96B70-F1	66.33	0.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 75 (showing top): AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, HFH4_01, E4F1_Q6, GATA4_Q3, CREBP1CJUN_01, RNCTGNYNRNCTGNY_UNKNOWN, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN, TEF_Q6, MARTENS_TRETINOIN_RESPONSE_DN, RP58_01, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C, GSE14415_INDUCED_VS_NATURAL_TREG_UP, HOXA10_TARGET_GENES, ID2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
cation binding	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LENG9	CDC42EP5	Q6NZY7	636
LENG9	LENG8	Q96PV6	614
LENG9	TTYH1	Q9H313	551
LENG9	DENND10	Q8TCE6	425
LENG9	ZC3HAV1L	Q96H79	420
LENG9	TMCO4	Q5TGY1	419
LENG9	PHYHIP	Q92561	417
LENG9	ASCC1	Q8N9N2	417
LENG9	TARM1	B6A8C7	413
LENG9	ZMAT4	Q9H898	409
LENG9	LENG1	Q96BZ8	404
LENG9	GLB1L2	Q8IW92	391
LENG9	LAIR1	Q6GTX8	386
LENG9	C1orf159	Q96HA4	369
LENG9	RBM26	Q5T8P6	363

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CARNMT1	NUP42	psi-mi:“MI:0914”(association)	0.640
FOXS1	DDX39A	psi-mi:“MI:0914”(association)	0.350
CDC5L		psi-mi:“MI:0914”(association)	0.350

BioGRID (10): LENG9 (Affinity Capture-MS), LENG9 (Affinity Capture-MS), LENG9 (Affinity Capture-MS), LENG9 (Affinity Capture-MS), LENG9 (Reconstituted Complex), LENG9 (Affinity Capture-MS), LENG9 (Affinity Capture-MS), LENG9 (Affinity Capture-MS), LENG9 (Affinity Capture-MS), LENG9 (Protein-RNA)

ESM2 similar proteins: A4GXA9, A7E3N7, A8VU90, D3KCC4, D3ZZN9, G3V8H4, O08672, O95382, Q13608, Q13671, Q14296, Q17RN3, Q28616, Q3UR50, Q3UR97, Q3V3V9, Q4KM32, Q53GL7, Q56A04, Q58CQ5, Q58EX7, Q5BK61, Q5NVA9, Q62893, Q643R3, Q66H85, Q6F5E8, Q6NVH7, Q6ZW31, Q7T0L4, Q80UU1, Q80XL1, Q8BJW7, Q8BTN6, Q8CIE4, Q8CJ00, Q8K592, Q8N2G8, Q8NAG6, Q8VCI7

Diamond homologs: O15504, Q5RB98, Q8BTN6, Q96B70

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	119
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

44 predictions. Top by Δscore:

Variant	Effect	Δscore
19:54463492:T:TA	donor_gain	0.6000
19:54462760:T:TA	donor_gain	0.4400
19:54462835:C:G	acceptor_gain	0.4400
19:54463133:C:CT	acceptor_gain	0.4300
19:54463263:G:C	donor_gain	0.4100
19:54463134:A:C	acceptor_gain	0.4000
19:54463262:AGC:A	donor_gain	0.3900
19:54463441:T:TA	donor_gain	0.3500
19:54463006:TCGG:T	donor_gain	0.3400
19:54463007:CGGC:C	donor_gain	0.3400
19:54463048:T:TA	donor_gain	0.3400
19:54462808:T:TA	donor_gain	0.3300
19:54463269:C:CT	donor_gain	0.3000
19:54463030:C:CA	donor_gain	0.2900
19:54462765:G:A	donor_gain	0.2700
19:54462809:C:A	donor_gain	0.2700
19:54462954:C:CA	donor_gain	0.2700
19:54462983:G:T	donor_gain	0.2700
19:54463082:C:CT	acceptor_gain	0.2700
19:54463266:C:CT	donor_gain	0.2700
19:54462979:T:TA	donor_gain	0.2600
19:54463262:AG:A	donor_gain	0.2600
19:54462745:C:CA	donor_gain	0.2500
19:54462922:T:TA	donor_gain	0.2500
19:54463068:T:TA	donor_gain	0.2500
19:54463321:T:TA	donor_gain	0.2500
19:54462040:T:A	donor_gain	0.2400
19:54462761:C:A	donor_gain	0.2400
19:54463069:C:A	donor_gain	0.2400
19:54463141:C:CT	acceptor_gain	0.2400

AlphaMissense

3017 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000015318 (19:54465694 G>A), RS1000128531 (19:54461898 T>C), RS1000338246 (19:54464182 C>T), RS1000481171 (19:54462022 A>G,T), RS1001362910 (19:54464228 G>A), RS1001394184 (19:54464388 G>A), RS10017 (19:54465172 C>A,T), RS1002589142 (19:54461267 G>A,C), RS1003119682 (19:54464556 C>CG), RS1003131003 (19:54464407 CTG>C), RS1003477553 (19:54463534 G>A), RS1003622646 (19:54461483 C>T), RS1003729542 (19:54465138 T>C), RS1003946265 (19:54465740 A>G), RS1004124365 (19:54465242 C>A,G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): myoepithelial tumor (MONDO:0002380)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D009208	Myoepithelioma	C04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	increases expression	1
jinfukang	increases expression	1
Glyphosate	decreases expression	1
Air Pollutants	increases expression, increases abundance	1
Cisplatin	increases expression	1
Glucose	decreases expression	1
Niclosamide	increases expression	1
Smoke	increases abundance, increases expression	1
Urethane	decreases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03600649	PHASE1	UNKNOWN	Clinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196	PHASE1/PHASE2	UNKNOWN	A Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272	PHASE1/PHASE2	RECRUITING	NRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190	PHASE1/PHASE2	RECRUITING	Alpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420	Not specified	COMPLETED	Malignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis