LBHD1

Summary

LBHD1 (LBH domain containing 1, HGNC:28351) is a protein-coding gene on chromosome 11q12.3, encoding LBH domain-containing protein 1 (Q9BQE6).

This gene shares three exons in common with another gene, chromosome 11 open reading frame 98 (GeneID:102288414), but the encoded protein uses a reading frame that is different from that of the chromosome 11 open reading frame 98 gene.

Source: NCBI Gene 79081 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 70 total — 1 pathogenic
• MANE Select transcript: NM_024099

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28351
Approved symbol	LBHD1
Name	LBH domain containing 1
Location	11q12.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC2477
Ensembl gene	ENSG00000162194
Ensembl biotype	protein_coding
Entrez	79081

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000354588, ENST00000377954, ENST00000415855, ENST00000431002, ENST00000524759, ENST00000526490, ENST00000527679, ENST00000528115, ENST00000528862, ENST00000532208

RefSeq mRNA: 12 — MANE Select: NM_024099 NM_001367940, NM_001367941, NM_001394596, NM_001394599, NM_001394601, NM_001394604, NM_001394606, NM_001394607, NM_001394609, NM_001394611, NM_001394612, NM_024099

CCDS: CCDS8028, CCDS91492

Canonical transcript exons

ENST00000354588 — 7 exons

Exon	Start	End
ENSE00001278511	62671564	62672267
ENSE00003468019	62669641	62669803
ENSE00003482876	62667523	62667747
ENSE00003543286	62669882	62670041
ENSE00003606996	62664849	62664973
ENSE00003650502	62662817	62663159
ENSE00003671898	62663236	62663333

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 84.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6997 / max 983.4450, expressed in 1419 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120192	6.2782	651
120190	1.5649	989
120193	0.5229	259
120194	0.3017	157
120191	0.0320	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	84.55	gold quality
right adrenal gland cortex	UBERON:0035827	83.37	gold quality
right adrenal gland	UBERON:0001233	82.55	gold quality
bone marrow cell	CL:0002092	81.44	gold quality
mucosa of transverse colon	UBERON:0004991	79.94	gold quality
left adrenal gland	UBERON:0001234	79.89	gold quality
adrenal gland	UBERON:0002369	79.69	gold quality
left adrenal gland cortex	UBERON:0035825	79.57	gold quality
bone marrow	UBERON:0002371	79.47	gold quality
spleen	UBERON:0002106	79.29	gold quality
sural nerve	UBERON:0015488	79.09	gold quality
lymph node	UBERON:0000029	78.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.43	gold quality
tonsil	UBERON:0002372	77.83	gold quality
adrenal tissue	UBERON:0018303	77.50	gold quality
right lobe of liver	UBERON:0001114	77.09	gold quality
blood	UBERON:0000178	76.70	gold quality
leukocyte	CL:0000738	76.64	gold quality
vermiform appendix	UBERON:0001154	76.59	gold quality
monocyte	CL:0000576	76.51	gold quality
rectum	UBERON:0001052	76.38	gold quality
stromal cell of endometrium	CL:0002255	76.10	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.88	gold quality
ventricular zone	UBERON:0003053	75.45	gold quality
liver	UBERON:0002107	75.02	gold quality
small intestine	UBERON:0002108	74.69	gold quality
transverse colon	UBERON:0001157	74.67	gold quality
duodenum	UBERON:0002114	74.57	gold quality
small intestine Peyer’s patch	UBERON:0003454	74.57	gold quality
lower esophagus mucosa	UBERON:0035834	74.55	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9543	yes	42.68
E-CURD-112	yes	13.96
E-HCAD-13	no	2.93
E-ANND-3	no	2.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting LBHD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-4695-5P	99.06	64.87	1151
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-4266	98.53	67.29	1035
HSA-MIR-3158-3P	98.45	64.25	560
HSA-MIR-3190-3P	97.61	66.95	1406
HSA-MIR-15A-3P	97.47	65.08	527
HSA-MIR-5704	94.82	67.46	448

Cross-species orthologs

0 orthologs

Paralogs (1): LBH (ENSG00000213626)

Protein

Protein identifiers

LBH domain-containing protein 1 — Q9BQE6 (reviewed: Q9BQE6)

All UniProt accessions (4): E9PMK4, E9PQ29, F5H6J2, Q9BQE6

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in bladder cancer tissues (at protein level).

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BQE6-1	1	yes
Q9BQE6-2	2

RefSeq proteins (12): NP_001354869, NP_001354870, NP_001381525, NP_001381528, NP_001381530, NP_001381533, NP_001381535, NP_001381536, NP_001381538, NP_001381540, NP_001381541, NP_077004* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038990	LBH_dom	Domain
IPR042945	LBH_dom_prot	Family

Pfam: PF15317

UniProt features (6 total): region of interest 2, chain 1, domain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQE6-F1	49.51	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (1): positive regulation of DNA-templated transcription (GO:0045893)

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

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

158 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LBHD1	CRAMP1	Q96RY5	637
LBHD1	ZNF512B	Q96KM6	569
LBHD1	SFI1	A8K8P3	569
LBHD1	CRYM	Q14894	557
LBHD1	THAP7	Q9BT49	532
LBHD1	NR0B2	Q15466	460
LBHD1	ANKFY1	Q9P2R3	417
LBHD1	TXNL1	O43396	357
LBHD1	UBB	P02248	223
LBHD1	NXNL2	Q5VZ03	220
LBHD1	SEC14L2	O76054	206
LBHD1	NCOR1	O75376	186
LBHD1	HDAC3	O15379	180
LBHD1	MAPK8IP2	Q13387	175
LBHD1	GLRX3	O76003	167

IntAct

6 interactions, top by confidence:

A	B	Type	Score
ERBB3	LBHD1	psi-mi:“MI:0915”(physical association)	0.370
HSPB1	LBHD1	psi-mi:“MI:0915”(physical association)	0.370
LBHD1	AURKA	psi-mi:“MI:0914”(association)	0.350
	IPO5	psi-mi:“MI:0914”(association)	0.350
LYAR	LBHD1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): LBHD1 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), AURKA (Affinity Capture-MS), FNTB (Affinity Capture-MS), OBSL1 (Affinity Capture-MS), CTU1 (Affinity Capture-MS), STRADA (Affinity Capture-MS), LBHD1 (Two-hybrid), LBHD1 (Two-hybrid), AURKA (Affinity Capture-MS), CTU1 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), NADSYN1 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8I316, A0A1W2PR82, A0A286YDK6, A5PJD3, A6H7B4, A6NEV1, A6NGY1, A6NHS1, A6QP24, A8MUA0, A8MUI8, A8MV72, A8MX80, A8MYA2, D3ZAQ5, O60393, P0C1T1, P0DL12, P43359, Q0KK55, Q0VD86, Q1RN00, Q32LI3, Q3UN58, Q3ZCQ2, Q5M831, Q5M844, Q66H53, Q68US1, Q6AYA8, Q6DIA7, Q6K1E7, Q6PE65, Q6ZW13, Q80VY2, Q8BII1, Q8IY42, Q8N9G6, Q8NA77, Q8TDR4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	48
Likely benign	12
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
161120	NM_001085372.3(UQCC3):c.59T>A (p.Val20Glu)	Pathogenic

SpliceAI

2098 predictions. Top by Δscore:

Variant	Effect	Δscore
11:62663232:TCA:T	donor_loss	1.0000
11:62663234:A:T	donor_loss	1.0000
11:62663235:C:A	donor_loss	1.0000
11:62663238:T:A	donor_gain	1.0000
11:62663329:TGGAC:T	acceptor_gain	1.0000
11:62663331:GAC:G	acceptor_gain	1.0000
11:62663332:AC:A	acceptor_gain	1.0000
11:62663333:CC:C	acceptor_gain	1.0000
11:62663333:CCTGA:C	acceptor_gain	1.0000
11:62663334:C:CA	acceptor_loss	1.0000
11:62663334:C:CC	acceptor_gain	1.0000
11:62663334:C:CG	acceptor_loss	1.0000
11:62663337:A:AC	acceptor_gain	1.0000
11:62663341:G:C	acceptor_gain	1.0000
11:62663341:G:GC	acceptor_gain	1.0000
11:62663345:G:C	acceptor_gain	1.0000
11:62663345:G:GC	acceptor_gain	1.0000
11:62664843:A:AC	donor_gain	1.0000
11:62664844:C:CC	donor_gain	1.0000
11:62664846:TA:T	donor_loss	1.0000
11:62664846:TACG:T	donor_loss	1.0000
11:62664847:A:AC	donor_gain	1.0000
11:62664847:ACG:A	donor_gain	1.0000
11:62664847:ACGC:A	donor_gain	1.0000
11:62664847:ACGCC:A	donor_gain	1.0000
11:62664848:C:CA	donor_gain	1.0000
11:62664848:CG:C	donor_gain	1.0000
11:62664848:CGC:C	donor_gain	1.0000
11:62664848:CGCC:C	donor_gain	1.0000
11:62664848:CGCCC:C	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000900240 (11:62667298 A>G), RS1001041985 (11:62662455 T>C), RS1001255103 (11:62667674 G>C,T), RS1001545821 (11:62672222 C>T), RS1002205940 (11:62672661 G>C), RS1002570642 (11:62672533 G>A,C,T), RS1002647003 (11:62668148 C>A), RS1002810598 (11:62673958 G>A), RS1002952502 (11:62671097 C>G), RS1003009191 (11:62665794 C>A,T), RS1003158617 (11:62671327 C>G,T), RS1003167972 (11:62674163 G>A), RS1003195972 (11:62664525 T>C), RS1003659267 (11:62664236 T>C), RS1003908696 (11:62671599 T>C,G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:616111

GenCC curated gene-disease

Mondo (1): mitochondrial complex III deficiency nuclear type 9 (MONDO:0014496)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST005956_12	Waist-to-hip ratio adjusted for BMI	2.000000e-06
GCST005956_2	Waist-to-hip ratio adjusted for BMI	1.000000e-08
GCST005962_37	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	5.000000e-07
GCST005962_51	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-07
GCST90002399_65	Neutrophil percentage of white cells	6.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bufotalin	decreases expression	1
bisphenol A	decreases methylation	1
beta-lapachone	increases expression	1
cobaltous chloride	decreases expression	1
ferrous chloride	decreases expression	1
chloropicrin	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Diazinon	increases methylation	1
Ethyl Methanesulfonate	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Ozone	affects expression, increases abundance	1
Phthalic Acids	increases methylation	1
Selenium	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Vitamin E	affects cotreatment, decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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