SMIM29

Summary

SMIM29 (small integral membrane protein 29, HGNC:1340) is a protein-coding gene on chromosome 6p21.31, encoding Small integral membrane protein 29 (Q86T20).

Predicted to be located in membrane.

Source: NCBI Gene 221491 — RefSeq curated summary.

At a glance

• GWAS associations: 56
• Clinical variants (ClinVar): 41 total
• MANE Select transcript: NM_001008703

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1340
Approved symbol	SMIM29
Name	small integral membrane protein 29
Location	6p21.31
Locus type	gene with protein product
Status	Approved
Aliases	LBH, MGC57858
Ensembl gene	ENSG00000186577
Ensembl biotype	protein_coding
OMIM	611419
Entrez	221491

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 15 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000394990, ENST00000413013, ENST00000463083, ENST00000468145, ENST00000476320, ENST00000481533, ENST00000495581, ENST00000636500, ENST00000637920, ENST00000858098, ENST00000858099, ENST00000858100, ENST00000858101, ENST00000928385, ENST00000928386, ENST00000928387, ENST00000928388, ENST00000928389, ENST00000957852

RefSeq mRNA: 4 — MANE Select: NM_001008703 NM_001008703, NM_001008704, NM_001287396, NM_178508

CCDS: CCDS4790, CCDS93896

Canonical transcript exons

ENST00000476320 — 5 exons

Exon	Start	End
ENSE00001865540	34248979	34249006
ENSE00003795378	34247467	34247492
ENSE00003795699	34247044	34247149
ENSE00003799698	34247681	34247864
ENSE00003800566	34246395	34246868

Expression profiles

Bgee: expression breadth ubiquitous, 225 present calls, max score 97.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.0460 / max 121.7202, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73225	23.6685	1815
73226	0.3775	176

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
anterior cingulate cortex	UBERON:0009835	97.89	gold quality
amygdala	UBERON:0001876	97.75	gold quality
hypothalamus	UBERON:0001898	97.68	gold quality
right frontal lobe	UBERON:0002810	97.46	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.04	gold quality
prefrontal cortex	UBERON:0000451	96.96	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.92	gold quality
spinal cord	UBERON:0002240	96.17	gold quality
substantia nigra	UBERON:0002038	95.80	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.52	gold quality
midbrain	UBERON:0001891	95.11	gold quality
putamen	UBERON:0001874	95.05	gold quality
nucleus accumbens	UBERON:0001882	94.99	gold quality
frontal cortex	UBERON:0001870	94.96	gold quality
tibial nerve	UBERON:0001323	94.74	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.73	gold quality
neocortex	UBERON:0001950	94.69	gold quality
skin of leg	UBERON:0001511	94.65	gold quality
caudate nucleus	UBERON:0001873	94.58	gold quality
apex of heart	UBERON:0002098	94.56	gold quality
skin of abdomen	UBERON:0001416	94.39	gold quality
cerebellar hemisphere	UBERON:0002245	94.25	gold quality
cerebellar cortex	UBERON:0002129	94.17	gold quality
forebrain	UBERON:0001890	93.45	gold quality
adenohypophysis	UBERON:0002196	93.42	gold quality
cerebral cortex	UBERON:0000956	93.38	gold quality
brain	UBERON:0000955	93.33	gold quality
cerebellum	UBERON:0002037	93.32	gold quality
granulocyte	CL:0000094	93.11	gold quality
lower esophagus mucosa	UBERON:0035834	93.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.93
E-MTAB-2983	no	140.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting SMIM29, 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-1277-5P	100.00	73.95	5056
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-449B-3P	99.20	67.24	1047
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-661	99.09	65.94	2062

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim29	ENSDARG00000090634
mus_musculus	Smim29	ENSMUSG00000062753
rattus_norvegicus	Smim29	ENSRNOG00000054374

Paralogs (1): C3orf18 (ENSG00000088543)

Protein

Protein identifiers

Small integral membrane protein 29 — Q86T20 (reviewed: Q86T20)

Alternative names: Protein LBH

All UniProt accessions (4): Q86T20, A0A2U3TZT1, G8JLJ3, L8E8G6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed in spleen, thymus, prostate, testis, uterus, small intestine, colon and peripheral blood leukocytes.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86T20-1	1	yes
Q86T20-2	2

RefSeq proteins (4): NP_001008703, NP_001008704, NP_001274325, NP_848603 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR043239	SMIM29	Family

UniProt features (4 total): chain 1, transmembrane region 1, glycosylation site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86T20-F1	71.70	0.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 3

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 331 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_SOMATIC_STEM_CELL_POPULATION_MAINTENANCE, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_CELLULAR_RESPONSE_TO_LIPID, PEREZ_TP63_TARGETS, GOBP_NEGATIVE_REGULATION_OF_STEM_CELL_DIFFERENTIATION, ATACCTC_MIR202, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_MAMMARY_GLAND_EPITHELIUM_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_ESTROGEN_RECEPTOR_SIGNALING_PATHWAY, MODULE_493, GOBP_REGULATION_OF_INTRACELLULAR_STEROID_HORMONE_RECEPTOR_SIGNALING_PATHWAY, GOBP_MAMMARY_GLAND_EPITHELIAL_CELL_DIFFERENTIATION, BRUECKNER_TARGETS_OF_MIRLET7A3_DN

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SLC1A6	ILVBL	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): C6orf1 (Two-hybrid), C6orf1 (Affinity Capture-MS), C6orf1 (Proximity Label-MS), C6orf1 (Proximity Label-MS), C6orf1 (Proximity Label-MS), C6orf1 (Proximity Label-MS), C6orf1 (Proximity Label-MS), C6orf1 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GVV1, A0M8S0, A0M8T1, A3KN28, A4D7R9, A9JRA0, E1BD52, E9Q2Z6, O55003, Q00PJ0, Q07DV5, Q07DW9, Q07DX8, Q07DY8, Q07E08, Q07E45, Q08CB3, Q09YH4, Q09YI5, Q09YJ7, Q09YK8, Q09YN2, Q108U3, Q2IBA8, Q2IBD0, Q2IBE0, Q2IBE8, Q2QL86, Q2QLA6, Q2QLB7, Q2QLD7, Q2QLE8, Q2QLG2, Q32KN2, Q5JRV8, Q5T292, Q5XII8, Q68FW3, Q86T20, Q8K4P7

Diamond homologs: Q86T20, Q8BGK9, Q8R043, Q9UK00

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1295 predictions. Top by Δscore:

Variant	Effect	Δscore
2:30232750:G:GT	donor_gain	1.0000
2:30234399:T:A	acceptor_gain	1.0000
2:30234401:GCAGC:G	acceptor_loss	1.0000
2:30234402:CAGC:C	acceptor_loss	1.0000
2:30234403:A:AG	acceptor_gain	1.0000
2:30234403:AG:A	acceptor_loss	1.0000
2:30234404:G:GT	acceptor_gain	1.0000
2:30234404:GC:G	acceptor_gain	1.0000
2:30234404:GCC:G	acceptor_gain	1.0000
2:30234404:GCCC:G	acceptor_gain	1.0000
2:30234404:GCCCC:G	acceptor_gain	1.0000
2:30234508:G:GA	donor_loss	1.0000
2:30234508:G:GG	donor_gain	1.0000
2:30234510:GA:G	donor_gain	1.0000
2:30234512:G:GG	donor_gain	1.0000
6:34247039:CTCA:C	donor_loss	1.0000
6:34247041:CA:C	donor_loss	1.0000
6:34247042:A:AC	donor_gain	1.0000
6:34247043:C:CC	donor_gain	1.0000
6:34247043:C:CT	donor_loss	1.0000
6:34247145:CCACC:C	acceptor_gain	1.0000
6:34247146:CACC:C	acceptor_gain	1.0000
6:34247146:CACCC:C	acceptor_gain	1.0000
6:34247148:CC:C	acceptor_gain	1.0000
6:34247149:CC:C	acceptor_gain	1.0000
6:34247150:C:CC	acceptor_gain	1.0000
6:34247150:C:T	acceptor_gain	1.0000
6:34247734:AGC:A	donor_gain	1.0000
2:30231711:G:T	donor_gain	0.9900
2:30231765:G:GA	donor_loss	0.9900

AlphaMissense

668 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:34247698:C:G	G32R	0.990
6:34247698:C:T	G32R	0.990
6:34247685:G:T	A36D	0.989
6:34247126:A:G	L54P	0.985
6:34247697:C:T	G32E	0.985
6:34247135:C:G	R51P	0.969
6:34247138:A:G	L50P	0.964
6:34247121:G:A	P56S	0.961
6:34247721:G:C	P24R	0.958
6:34247730:A:T	V21E	0.958
6:34247123:A:G	L55P	0.956
6:34247703:A:C	L30R	0.954
6:34247712:A:C	L27R	0.950
6:34247121:G:T	P56T	0.949
6:34247136:G:T	R51S	0.949
6:34247120:G:T	P56H	0.946
6:34247115:A:G	Y58H	0.945
6:34247694:A:T	V33E	0.936
6:34247467:C:G	R46P	0.933
6:34247709:A:T	I28N	0.928
6:34247126:A:T	L54Q	0.927
6:34247712:A:T	L27H	0.925
6:34247141:C:G	R49P	0.922
6:34247706:G:T	T29N	0.922
6:34247120:G:C	P56R	0.921
6:34247691:A:T	V34E	0.921
6:34247114:T:G	Y58S	0.920
6:34247115:A:C	Y58D	0.920
6:34247721:G:T	P24H	0.920
6:34247114:T:C	Y58C	0.918

dbSNP variants (sampled 300 via entrez): RS1000396258 (6:34246423 A>G), RS1001219180 (6:34249371 C>G), RS1001314162 (6:34249913 C>T), RS1002157975 (6:34246927 C>T), RS1003898503 (6:34249875 A>G), RS1005117454 (6:34249094 C>T), RS1006156506 (6:34248122 A>G), RS1007158885 (6:34247475 C>T), RS1007220221 (6:34250689 T>C,G), RS10080749 (6:34250388 A>G), RS1008154682 (6:34246331 G>A,C), RS1008527532 (6:34247928 C>T), RS1009024967 (6:34248292 T>A,C), RS1009445570 (6:34250257 C>T), RS1009497993 (6:34250657 A>C)

Disease associations

OMIM: gene MIM:611419 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

56 associations (top):

Study	Trait	p-value
GCST000175_38	Height	1.000000e-08
GCST000522_11	Height	2.000000e-08
GCST000987_4	Celiac disease or Rheumatoid arthritis	1.000000e-08
GCST001188_11	vWF and FVIII levels	1.000000e-06
GCST002284_23	QRS duration in Tripanosoma cruzi seropositivity	8.000000e-07
GCST002318_149	Rheumatoid arthritis	1.000000e-09
GCST002318_23	Rheumatoid arthritis	4.000000e-08
GCST003129_21	Primary biliary cholangitis	5.000000e-08
GCST003174_10	Sense of smell	6.000000e-06
GCST003174_17	Sense of smell	6.000000e-06
GCST003174_9	Sense of smell	7.000000e-06
GCST003622_13	Systemic lupus erythematosus	1.000000e-09
GCST003622_14	Systemic lupus erythematosus	2.000000e-16
GCST003622_4	Systemic lupus erythematosus	6.000000e-06
GCST003622_5	Systemic lupus erythematosus	1.000000e-08
GCST003622_60	Systemic lupus erythematosus	2.000000e-09
GCST004212_20	Height	5.000000e-11
GCST005752_6	Systemic lupus erythematosus	5.000000e-08
GCST005951_153	Body mass index	5.000000e-09
GCST005984_19	Glomerular filtration rate	2.000000e-09
GCST006048_30	Rheumatoid arthritis (ACPA-positive)	4.000000e-09
GCST006061_128	Atrial fibrillation	4.000000e-08
GCST006920_1	Regular attendance at a gym or sports club	4.000000e-08
GCST006959_168	Rheumatoid arthritis	3.000000e-09
GCST006959_40	Rheumatoid arthritis	1.000000e-07
GCST007344_99	Estimated glomerular filtration rate	2.000000e-10
GCST007490_14	Anthropometric traits (multi-trait analysis)	2.000000e-69
GCST008644_20	Celiac disease and Rheumatoid arthritis	2.000000e-08
GCST008839_202	Height	7.000000e-14
GCST009597_12	Multiple sclerosis	7.000000e-10

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004630	factor VIII measurement
EFO:0004340	body mass index
EFO:0009592	social interaction measurement
EFO:0004324	body weights and measures
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0004833	neutrophil count
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	decreases expression, increases expression	3
Cyclosporine	increases expression	2
GSK-J4	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
yessotoxin	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
jinfukang	increases expression	1
PP242	increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases expression	1
Doxorubicin	increases expression	1
Flame Retardants	increases expression	1
Hydrogen Peroxide	affects expression	1
N-Nitrosopyrrolidine	increases expression	1
Quercetin	increases expression	1
Smoke	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Urethane	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
Acrylamide	decreases expression	1
Vitamin K 3	affects expression	1
Halogenated Diphenyl Ethers	increases expression	1

Clinical trials (associated diseases)

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