SMIM11

Summary

SMIM11 (small integral membrane protein 11, HGNC:1293) is a protein-coding gene on chromosome 21q22.11-q22.12, encoding Small integral membrane protein 11 (P58511).

Predicted to be located in membrane.

Source: NCBI Gene 54065 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_058182

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1293
Approved symbol	SMIM11
Name	small integral membrane protein 11
Location	21q22.11-q22.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205670
Ensembl biotype	protein_coding
Entrez	54065

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 17 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000399292, ENST00000399295, ENST00000399299, ENST00000474455, ENST00000481710, ENST00000489469, ENST00000495363, ENST00000652570, ENST00000895992, ENST00000895993, ENST00000895994, ENST00000895995, ENST00000895996, ENST00000895997, ENST00000895998, ENST00000895999, ENST00000896000, ENST00000927396, ENST00000927397, ENST00000927398, ENST00000927399

RefSeq mRNA: 4 — MANE Select: NM_058182 NM_001376899, NM_001394150, NM_001394152, NM_058182

CCDS: CCDS33550

Canonical transcript exons

ENST00000399292 — 4 exons

Exon	Start	End
ENSE00000000299	34375507	34375567
ENSE00001537374	34388629	34389151
ENSE00003525225	34385478	34385644
ENSE00003674919	34379428	34379516

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 92.29.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of stomach	UBERON:0001161	92.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.24	gold quality
fundus of stomach	UBERON:0001160	90.85	gold quality
nucleus accumbens	UBERON:0001882	90.73	gold quality
stomach	UBERON:0000945	90.65	gold quality
prefrontal cortex	UBERON:0000451	90.41	gold quality
putamen	UBERON:0001874	90.27	gold quality
gastrocnemius	UBERON:0001388	89.84	gold quality
muscle of leg	UBERON:0001383	89.70	gold quality
islet of Langerhans	UBERON:0000006	89.61	gold quality
anterior cingulate cortex	UBERON:0009835	89.57	gold quality
amygdala	UBERON:0001876	89.56	gold quality
temporal lobe	UBERON:0001871	89.46	gold quality
Ammon’s horn	UBERON:0001954	89.40	gold quality
caudate nucleus	UBERON:0001873	89.25	gold quality
hypothalamus	UBERON:0001898	89.11	gold quality
muscle tissue	UBERON:0002385	89.11	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.10	gold quality
substantia nigra	UBERON:0002038	89.09	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.05	gold quality
frontal cortex	UBERON:0001870	89.04	gold quality
cortical plate	UBERON:0005343	89.02	gold quality
skeletal muscle tissue	UBERON:0001134	88.99	gold quality
cerebral cortex	UBERON:0000956	88.94	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.74	gold quality
brain	UBERON:0000955	88.09	gold quality
heart left ventricle	UBERON:0002084	87.88	gold quality
smooth muscle tissue	UBERON:0001135	87.38	gold quality
right frontal lobe	UBERON:0002810	87.22	gold quality
heart	UBERON:0000948	86.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting SMIM11, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-9903	98.47	66.70	748
HSA-MIR-6780A-3P	98.42	67.49	1518
HSA-MIR-6730-5P	98.03	68.12	1299
HSA-MIR-876-5P	97.99	68.49	1345
HSA-MIR-6787-3P	97.75	66.17	1233
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-3167	96.81	67.09	1236
HSA-MIR-500B-3P	96.49	65.40	1087

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim11	ENSMUSG00000051989
rattus_norvegicus	Smim11	ENSRNOG00000039877

Protein

Protein identifiers

Small integral membrane protein 11 — P58511 (reviewed: P58511)

All UniProt accessions (2): A0A8C8KJI4, P58511

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed in heart, spleen, liver, stomach, muscle, lung, testis, skin, PBL and bone marrow.

RefSeq proteins (7): NP_001300621, NP_001363828, NP_001381079, NP_001381080, NP_001381081, NP_001381082, NP_478062* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042125	SMIM11	Family

Pfam: PF14981

UniProt features (4 total): chain 1, transmembrane region 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P58511-F1	82.10	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, VECCHI_GASTRIC_CANCER_EARLY_DN, MARKEY_RB1_ACUTE_LOF_UP, chr21q22, TCCCRNNRTGC_UNKNOWN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP, GCNP_SHH_UP_LATE.V1_UP, MIR4795_3P, GSE10240_IL22_VS_IL22_AND_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP

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

246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM11	RUNX1	Q01196	427
SMIM11	C21orf58	P58505	400
SMIM11	RGPD1	P0C839	393
SMIM11	MTRES1	Q9P0P8	376
SMIM11	PAXBP1	Q9Y5B6	375
SMIM11	MAP3K7CL	P57077	367
SMIM11	CEACAM20	Q6UY09	367
SMIM11	NIPSNAP3B	Q9BS92	354
SMIM11	SLX9	Q9NSI2	349
SMIM11	SWT1	Q5T5J6	340
SMIM11	YBEY	P58557	336
SMIM11	ZC4H2	Q9NQZ6	336
SMIM11	UNC5CL	Q8IV45	330
SMIM11	EVA1C	P58658	328
SMIM11	LAS1L	Q9Y4W2	327

IntAct

20 interactions, top by confidence:

A	B	Type	Score
ASPH	SMIM11	psi-mi:“MI:0915”(physical association)	0.560
SMIM11	UBQLN2	psi-mi:“MI:0915”(physical association)	0.560
SMIM11	ASPH	psi-mi:“MI:0915”(physical association)	0.560
SMIM11	CERS4	psi-mi:“MI:0915”(physical association)	0.560
MT1HL1	SMIM11	psi-mi:“MI:0915”(physical association)	0.400
UNC93B1		psi-mi:“MI:0914”(association)	0.350
COPB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
COPE	ESYT2	psi-mi:“MI:0914”(association)	0.350
COPZ1	ATL3	psi-mi:“MI:0914”(association)	0.350
KLRC2	CLGN	psi-mi:“MI:0914”(association)	0.350
IFNGR2	RTN2	psi-mi:“MI:0914”(association)	0.350
SMIM11	ATP5F1B	psi-mi:“MI:0914”(association)	0.350
SLC39A11	ESYT2	psi-mi:“MI:0914”(association)	0.350
TMBIM4	SMIM11	psi-mi:“MI:0915”(physical association)	0.000
SMIM11	UBQLN2	psi-mi:“MI:0915”(physical association)	0.000
SMIM11	CERS4	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (21): SMIM11 (Two-hybrid), SMIM11 (Affinity Capture-MS), SMIM11 (Two-hybrid), SMIM11 (Two-hybrid), SMIM11 (Two-hybrid), SMIM11 (Proximity Label-MS), SMIM11 (Affinity Capture-MS), TTYH3 (Affinity Capture-MS), SMIM11 (Affinity Capture-MS), ATP5B (Affinity Capture-MS), VMA21 (Affinity Capture-MS), SMIM11 (Affinity Capture-MS), SMIM11 (Affinity Capture-MS), SMIM11 (Affinity Capture-MS), SMIM11 (Negative Genetic)

ESM2 similar proteins: A0A1B0GQX3, A0A1B0GRQ0, A0A1B0GVT2, A0A590UK83, A4QNL6, A5D7B5, A6H770, B3DHH5, E1BAR0, O75324, P0DKX4, P35803, P56695, P58511, P61807, P61808, P84889, Q12016, Q15053, Q17Q87, Q28793, Q2TZ20, Q3MHM8, Q4V786, Q4V921, Q4VBG5, Q56JY4, Q5RBD8, Q5U2S1, Q68FV2, Q6DGP4, Q6GLN5, Q758B5, Q80Z96, Q80ZU4, Q876Z1, Q8BH07, Q8BT42, Q8GUM4, Q8R0W6

Diamond homologs: A6H770, P58511, Q99J19

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1528 predictions. Top by Δscore:

Variant	Effect	Δscore
21:34375568:G:GG	donor_gain	1.0000
21:34375563:GAGCA:G	donor_gain	0.9900
21:34375565:GCA:G	donor_gain	0.9900
21:34375594:G:GT	donor_gain	0.9900
21:34375864:A:T	donor_gain	0.9900
21:34375944:G:GT	donor_gain	0.9900
21:34375944:G:T	donor_gain	0.9900
21:34376181:T:G	donor_gain	0.9900
21:34379426:A:AG	acceptor_gain	0.9900
21:34379427:G:GG	acceptor_gain	0.9900
21:34375873:G:GT	donor_gain	0.9800
21:34375903:G:T	donor_gain	0.9800
21:34375838:TTC:T	donor_gain	0.9700
21:34379427:GATCA:G	acceptor_gain	0.9700
21:34375564:AGCAG:A	donor_loss	0.9600
21:34375565:GCAGT:G	donor_loss	0.9600
21:34375566:CA:C	donor_gain	0.9600
21:34375566:CAGT:C	donor_loss	0.9600
21:34375567:AGTA:A	donor_loss	0.9600
21:34375568:GTAA:G	donor_loss	0.9600
21:34375787:T:G	donor_gain	0.9600
21:34379512:GGAAG:G	donor_gain	0.9600
21:34379513:GAAGG:G	donor_gain	0.9600
21:34399740:G:C	acceptor_gain	0.9600
21:34402085:A:AG	acceptor_gain	0.9600
21:34375564:AGCA:A	donor_gain	0.9500
21:34375565:GCAG:G	donor_gain	0.9500
21:34375569:TAAG:T	donor_loss	0.9500
21:34375570:A:AG	donor_loss	0.9500
21:34375572:G:GG	donor_gain	0.9400

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000543679 (21:34375203 C>T), RS1001881486 (21:34374631 AC>A), RS1001933891 (21:34374369 T>C), RS1003944990 (21:34373973 C>A,T), RS1008067348 (21:34381411 A>G), RS1008468483 (21:34386828 T>C,G), RS1008853294 (21:34374072 C>A,T), RS1009454300 (21:34389426 C>T), RS1010083837 (21:34383965 C>G), RS1011518497 (21:34381524 A>C), RS1012771067 (21:34375692 G>C,T), RS1016803867 (21:34374277 C>T), RS1017439460 (21:34389649 T>C), RS1017765294 (21:34389488 G>T), RS1018229253 (21:34378235 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:613693

GenCC curated gene-disease

Mondo (1): long QT syndrome 6 (MONDO:0013370)

Orphanet (2): Romano-Ward syndrome (Orphanet:101016), Congenital long QT syndrome (Orphanet:768)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009391_1262	Metabolite levels	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004761	uric acid measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566333	Long Qt Syndrome 6 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment	2
entinostat	decreases expression, affects cotreatment	2
Benzo(a)pyrene	increases expression, increases methylation	2
Tetrachlorodibenzodioxin	increases expression	2
Tretinoin	decreases expression, increases expression	2
Cyclosporine	increases expression	2
ethyl-p-hydroxybenzoate	increases expression	1
benzo(e)pyrene	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Bortezomib	decreases expression	1
Amiodarone	increases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Estradiol	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methapyrilene	increases methylation	1
Nickel	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
S-Nitrosoglutathione	affects expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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