SMIM5

Summary

SMIM5 (small integral membrane protein 5, HGNC:40030) is a protein-coding gene on chromosome 17q25.1, encoding Small integral membrane protein 5 (Q71RC9).

Predicted to be located in membrane.

Source: NCBI Gene 643008 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001162995

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40030
Approved symbol	SMIM5
Name	small integral membrane protein 5
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204323
Ensembl biotype	protein_coding
Entrez	643008

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 22 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000375215, ENST00000537494, ENST00000581115, ENST00000910959, ENST00000910960, ENST00000910961, ENST00000910962, ENST00000910963, ENST00000910964, ENST00000910965, ENST00000910966, ENST00000910967, ENST00000910968, ENST00000910969, ENST00000941300, ENST00000941301, ENST00000941302, ENST00000941303, ENST00000941304, ENST00000941305, ENST00000941306, ENST00000941307, ENST00000941308

RefSeq mRNA: 1 — MANE Select: NM_001162995 NM_001162995

CCDS: CCDS54165

Canonical transcript exons

ENST00000375215 — 3 exons

Exon	Start	End
ENSE00001466215	75640791	75641404
ENSE00001637267	75640166	75640328
ENSE00001766449	75633434	75634202

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 98.50.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6973 / max 67.1691, expressed in 213 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
162758	0.3102	140
162759	0.1834	108
162757	0.1180	72
162753	0.0857	51

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	98.50	gold quality
kidney epithelium	UBERON:0004819	96.22	silver quality
lower esophagus mucosa	UBERON:0035834	94.29	gold quality
sural nerve	UBERON:0015488	93.63	gold quality
amniotic fluid	UBERON:0000173	92.91	gold quality
ileal mucosa	UBERON:0000331	91.60	gold quality
parotid gland	UBERON:0001831	91.38	silver quality
pharyngeal mucosa	UBERON:0000355	89.92	silver quality
right uterine tube	UBERON:0001302	89.85	gold quality
left ventricle myocardium	UBERON:0006566	89.45	gold quality
palpebral conjunctiva	UBERON:0001812	88.91	gold quality
trabecular bone tissue	UBERON:0002483	88.91	silver quality
renal medulla	UBERON:0000362	88.59	silver quality
esophagus squamous epithelium	UBERON:0006920	88.52	gold quality
gingival epithelium	UBERON:0001949	88.28	silver quality
cardiac muscle of right atrium	UBERON:0003379	88.03	gold quality
bronchial epithelial cell	CL:0002328	87.70	gold quality
oral cavity	UBERON:0000167	87.32	gold quality
gingiva	UBERON:0001828	87.26	silver quality
bronchus	UBERON:0002185	87.11	gold quality
tibial nerve	UBERON:0001323	86.89	gold quality
jejunal mucosa	UBERON:0000399	86.65	gold quality
metanephros cortex	UBERON:0010533	86.13	gold quality
esophagus mucosa	UBERON:0002469	85.58	gold quality
adult mammalian kidney	UBERON:0000082	84.62	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.61	gold quality
right lobe of thyroid gland	UBERON:0001119	84.40	gold quality
buccal mucosa cell	CL:0002336	84.36	gold quality
mammalian vulva	UBERON:0000997	84.32	silver quality
apex of heart	UBERON:0002098	84.16	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-MTAB-8498	yes	338.76
E-MTAB-10042	yes	35.02
E-HCAD-11	yes	21.15
E-HCAD-10	yes	14.64
E-ANND-3	yes	5.97
E-HCAD-9	yes	5.59
E-MTAB-9067	yes	3.11
E-MTAB-9467	no	0.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SMIM5, 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-12136	99.98	72.81	5713
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-422A	99.18	65.83	550
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-502-5P	98.77	66.51	906
HSA-MIR-378A-3P	98.43	66.10	548
HSA-MIR-378B	98.43	65.36	573
HSA-MIR-378C	98.43	66.10	548
HSA-MIR-378D	98.43	66.10	548
HSA-MIR-378E	98.43	65.99	551
HSA-MIR-378F	98.43	65.66	554
HSA-MIR-378H	98.43	66.16	545
HSA-MIR-378I	98.43	66.10	548
HSA-MIR-5088-5P	97.97	64.28	487
HSA-MIR-500A-3P	97.60	67.48	595
HSA-MIR-890	97.47	68.67	982
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-6895-5P	97.05	64.96	522
HSA-MIR-6772-3P	97.04	65.89	784
HSA-MIR-5194	96.77	63.91	1021
HSA-MIR-6762-5P	96.55	64.62	972
HSA-MIR-3654	96.43	66.55	646
HSA-MIR-6738-5P	96.33	63.61	815

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim5	ENSMUSG00000048442
rattus_norvegicus	Smim5	ENSRNOG00000049642

Protein

Protein identifiers

Small integral membrane protein 5 — Q71RC9 (reviewed: Q71RC9)

All UniProt accessions (1): Q71RC9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001156467* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031671	SMIM5/18/22	Family
IPR047133	SMIM5	Family

Pfam: PF15831

UniProt features (2 total): chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q71RC9-F1	77.09	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 75 (showing top): GOZGIT_ESR1_TARGETS_DN, IVANOVA_HEMATOPOIESIS_MATURE_CELL, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, FUJII_YBX1_TARGETS_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEN_METABOLIC_SYNDROM_NETWORK, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_UP, ZNF592_TARGET_GENES, MIR6868_5P, GSE11924_TH2_VS_TH17_CD4_TCELL_DN, MIR3654, GSE8685_IL2_STARVED_VS_IL21_ACT_IL2_STARVED_CD4_TCELL_UP, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_INFECTION_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

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM5	CYSRT1	A8MQ03	593
SMIM5	RIIAD1	A6NNX1	422
SMIM5	ERLN	P0DI80	418
SMIM5	DNAH6	Q9C0G6	413
SMIM5	PRR15L	Q9BU68	400
SMIM5	KRT78	Q8N1N4	396
SMIM5	RECQL5	O94762	380
SMIM5	TMEM212	A6NML5	378
SMIM5	TMEM95	Q3KNT9	375
SMIM5	GGT6	Q6P531	374
SMIM5	PRELID2	Q8N945	371
SMIM5	TMEM52B	Q4KMG9	360
SMIM5	MIER3	Q7Z3K6	359
SMIM5	C17orf50	Q8WW18	358
SMIM5	TMEM213	A2RRL7	357

IntAct

29 interactions, top by confidence:

A	B	Type	Score
SGTA	SMIM5	psi-mi:“MI:0915”(physical association)	0.600
ARFIP1	SMIM5	psi-mi:“MI:0915”(physical association)	0.560
SMIM5	PRRT2	psi-mi:“MI:0915”(physical association)	0.560
SMIM5	ZFYVE21	psi-mi:“MI:0915”(physical association)	0.560
SMIM5	SH3GLB1	psi-mi:“MI:0915”(physical association)	0.560
SMIM5	RBFA	psi-mi:“MI:0915”(physical association)	0.560
EHHADH	SMIM5	psi-mi:“MI:0915”(physical association)	0.560
SMIM5	KLRG2	psi-mi:“MI:0914”(association)	0.350
SMIM5	SGTA	psi-mi:“MI:0915”(physical association)	0.000
ARFIP1	SMIM5	psi-mi:“MI:0915”(physical association)	0.000
EHHADH	SMIM5	psi-mi:“MI:0915”(physical association)	0.000
RBFA	SMIM5	psi-mi:“MI:0915”(physical association)	0.000
PRRT2	SMIM5	psi-mi:“MI:0915”(physical association)	0.000
ZFYVE21	SMIM5	psi-mi:“MI:0915”(physical association)	0.000
SH3GLB1	SMIM5	psi-mi:“MI:0915”(physical association)	0.000
SGTA	SMIM5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (42): SMIM5 (Affinity Capture-MS), SMIM5 (Two-hybrid), SMIM5 (Two-hybrid), SMIM5 (Two-hybrid), SMIM5 (Two-hybrid), SMIM5 (Two-hybrid), SMIM5 (Two-hybrid), SMIM5 (Two-hybrid), SMIM5 (Affinity Capture-RNA), TMEM179B (Affinity Capture-MS), COLEC12 (Affinity Capture-MS), GALNT13 (Affinity Capture-MS), GP1BB (Affinity Capture-MS), LEMD3 (Affinity Capture-MS), FZD2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GST9, A0A1B0GTU2, A0A1B0GV90, A0A590UK83, A2RRL7, A7S641, A8WG88, A9JTJ0, B9X187, K7EJ46, O00168, O08589, O13001, P0C2S0, P15383, P41237, P56513, P60606, P63160, P63161, Q04645, Q04646, Q04679, Q04680, Q0P467, Q28EH9, Q3SZX0, Q3UJ81, Q3URE8, Q3ZBP2, Q4LDR2, Q4R6L9, Q502I1, Q592E4, Q5XF36, Q6AXF6, Q6NWH5, Q6PBK8, Q6Q3F5, Q71RC9

Diamond homologs: E1BAR0, Q71RC9, Q8BT42

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2407 predictions. Top by Δscore:

Variant	Effect	Δscore
17:75629744:A:AC	donor_gain	1.0000
17:75630157:C:A	donor_gain	1.0000
17:75630179:CCCA:C	donor_loss	1.0000
17:75630181:CA:C	donor_loss	1.0000
17:75630182:A:C	donor_loss	1.0000
17:75630183:C:T	donor_loss	1.0000
17:75630183:CCTT:C	donor_gain	1.0000
17:75630186:T:A	donor_gain	1.0000
17:75630273:CAGCT:C	acceptor_gain	1.0000
17:75630274:AGCT:A	acceptor_gain	1.0000
17:75630275:GCT:G	acceptor_gain	1.0000
17:75630276:CT:C	acceptor_gain	1.0000
17:75630276:CTC:C	acceptor_gain	1.0000
17:75630276:CTCTG:C	acceptor_loss	1.0000
17:75630277:TCT:T	acceptor_gain	1.0000
17:75630278:C:A	acceptor_gain	1.0000
17:75630278:C:CC	acceptor_gain	1.0000
17:75630280:G:C	acceptor_gain	1.0000
17:75630284:G:C	acceptor_gain	1.0000
17:75630284:G:GC	acceptor_gain	1.0000
17:75630287:C:CT	acceptor_gain	1.0000
17:75630617:A:AC	donor_gain	1.0000
17:75630618:C:CC	donor_gain	1.0000
17:75631144:CCTCA:C	donor_loss	1.0000
17:75631145:CTCAC:C	donor_loss	1.0000
17:75631146:TCAC:T	donor_loss	1.0000
17:75631147:CACCT:C	donor_loss	1.0000
17:75631148:A:C	donor_loss	1.0000
17:75631149:C:A	donor_loss	1.0000
17:75631245:CATAC:C	acceptor_gain	1.0000

AlphaMissense

485 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:75640322:T:C	F41L	0.956
17:75640324:C:A	F41L	0.956
17:75640324:C:G	F41L	0.956
17:75640304:T:C	F35L	0.949
17:75640306:C:A	F35L	0.949
17:75640306:C:G	F35L	0.949
17:75640311:T:A	V37D	0.934
17:75640302:C:A	A34D	0.924
17:75640323:T:C	F41S	0.920
17:75640797:T:A	V45D	0.911
17:75640261:G:C	K20N	0.896
17:75640261:G:T	K20N	0.896
17:75640251:T:C	L17P	0.883
17:75640326:C:A	T42K	0.880
17:75640299:T:A	V33E	0.864
17:75640305:T:C	F35S	0.862
17:75640263:T:C	L21P	0.861
17:75640800:T:G	L46R	0.861
17:75640322:T:A	F41I	0.844
17:75640320:T:G	L40R	0.836
17:75640323:T:G	F41C	0.836
17:75640326:C:G	T42R	0.830
17:75640820:T:C	C53R	0.829
17:75640818:C:A	A52D	0.828
17:75640227:A:T	E9V	0.824
17:75640251:T:A	L17Q	0.823
17:75640314:T:G	I38S	0.822
17:75640314:T:A	I38N	0.809
17:75640242:G:A	G14D	0.808
17:75640251:T:G	L17R	0.805

dbSNP variants (sampled 300 via entrez): RS1000045499 (17:75632266 G>A), RS1000059605 (17:75635014 C>T), RS1000333509 (17:75640066 T>C), RS1000872473 (17:75638649 CG>C,CGG), RS1001378645 (17:75639686 G>A), RS1001459861 (17:75633259 G>A), RS1001497845 (17:75634277 G>A), RS1001829817 (17:75635711 A>G), RS1002429286 (17:75638138 T>TAATTTTCC), RS1002504848 (17:75633007 A>C), RS1002785276 (17:75638359 T>C), RS1003380902 (17:75637024 G>A), RS1003513077 (17:75632010 T>A), RS1003784686 (17:75638605 C>T), RS1003846456 (17:75632310 GCAA>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sotorasib	decreases expression, affects cotreatment	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression, increases abundance	1
ethyl-p-hydroxybenzoate	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
hydroquinone	increases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	decreases expression	1
trametinib	decreases expression, affects cotreatment	1
(+)-JQ1 compound	decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, decreases expression	1
Cisplatin	decreases expression	1
Potassium Chloride	decreases expression, decreases response to substance	1
Smoke	increases abundance, increases expression	1
Dronabinol	decreases expression, decreases response to substance	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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