SMIM12

Summary

SMIM12 (small integral membrane protein 12, HGNC:25154) is a protein-coding gene on chromosome 1p34.3, encoding Small integral membrane protein 12 (Q96EX1).

Located in mitochondrion.

Source: NCBI Gene 113444 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 14 total
• MANE Select transcript: NM_138428

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25154
Approved symbol	SMIM12
Name	small integral membrane protein 12
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90372
Ensembl gene	ENSG00000163866
Ensembl biotype	protein_coding
Entrez	113444

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 20 protein_coding, 1 nonsense_mediated_decay

ENST00000417239, ENST00000423898, ENST00000426886, ENST00000446026, ENST00000456842, ENST00000521580, ENST00000910618, ENST00000910619, ENST00000910620, ENST00000940216, ENST00000940217, ENST00000940218, ENST00000940219, ENST00000940220, ENST00000940221, ENST00000952717, ENST00000952718, ENST00000952719, ENST00000952720, ENST00000952721, ENST00000952722

RefSeq mRNA: 4 — MANE Select: NM_138428 NM_001164824, NM_001164825, NM_001320261, NM_138428

CCDS: CCDS53295

Canonical transcript exons

ENST00000521580 — 2 exons

Exon	Start	End
ENSE00002243208	34850362	34855982
ENSE00002273915	34859677	34859749

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 95.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.4411 / max 91.6704, expressed in 1821 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11640	26.4411	1821

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	95.82	gold quality
tibialis anterior	UBERON:0001385	95.70	gold quality
islet of Langerhans	UBERON:0000006	93.95	gold quality
right lobe of liver	UBERON:0001114	93.93	gold quality
prefrontal cortex	UBERON:0000451	93.91	gold quality
popliteal artery	UBERON:0002250	93.91	gold quality
tibial artery	UBERON:0007610	93.90	gold quality
left adrenal gland	UBERON:0001234	93.89	gold quality
left adrenal gland cortex	UBERON:0035825	93.74	gold quality
mucosa of transverse colon	UBERON:0004991	93.64	gold quality
endothelial cell	CL:0000115	93.62	gold quality
right adrenal gland	UBERON:0001233	93.49	gold quality
heart left ventricle	UBERON:0002084	93.43	gold quality
left coronary artery	UBERON:0001626	93.41	gold quality
heart right ventricle	UBERON:0002080	93.40	gold quality
right adrenal gland cortex	UBERON:0035827	93.40	gold quality
cardiac ventricle	UBERON:0002082	93.31	gold quality
aorta	UBERON:0000947	93.28	gold quality
adrenal cortex	UBERON:0001235	93.23	gold quality
apex of heart	UBERON:0002098	93.20	gold quality
coronary artery	UBERON:0001621	93.08	gold quality
gastrocnemius	UBERON:0001388	92.90	gold quality
adrenal gland	UBERON:0002369	92.79	gold quality
right atrium auricular region	UBERON:0006631	92.67	gold quality
right coronary artery	UBERON:0001625	92.60	gold quality
thoracic aorta	UBERON:0001515	92.56	gold quality
heart	UBERON:0000948	92.55	gold quality
muscle of leg	UBERON:0001383	92.55	gold quality
left ventricle myocardium	UBERON:0006566	92.55	gold quality
ascending aorta	UBERON:0001496	92.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.74
E-GEOD-99795	no	127.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

129 targeting SMIM12, 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-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-383-3P	99.85	65.84	1359

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim12	ENSDARG00000070358
mus_musculus	Smim12	ENSMUSG00000042380
rattus_norvegicus	Smim12	ENSRNOG00000014352
drosophila_melanogaster	CG34228	FBGN0085257

Protein

Protein identifiers

Small integral membrane protein 12 — Q96EX1 (reviewed: Q96EX1)

All UniProt accessions (3): E5RH51, Q96EX1, L0R6D7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SMIM12 family.

RefSeq proteins (4): NP_001158296, NP_001158297, NP_001307190, NP_612437* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031933	UPF0767	Family

Pfam: PF15990

UniProt features (3 total): chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EX1-F1	77.92	0.29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, chr1p34, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, GSE14415_INDUCED_TREG_VS_TCONV_DN, ASH1L_TARGET_GENES, DIDO1_TARGET_GENES, DMRT1_TARGET_GENES, HOXC13_TARGET_GENES, LHX9_TARGET_GENES, NFKBIA_TARGET_GENES, SNIP1_TARGET_GENES, TEAD2_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (2): mitochondrion (GO:0005739), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2451 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM12	SHISA4	Q96DD7	650
SMIM12	BEND7	Q8N7W2	616
SMIM12	LRRC40	Q9H9A6	555
SMIM12	NAIF1	Q69YI7	536
SMIM12	ZC3H8	Q8N5P1	525
SMIM12	MOCS1	Q9NZB8	493
SMIM12	LCTL	Q6UWM7	490
SMIM12	CLEC2L	P0C7M8	472
SMIM12	TCAIM	Q8N3R3	459
SMIM12	MNMIP1	A4FU49	457
SMIM12	PAMR1	Q6UXH9	455
SMIM12	BTBD8	Q5XKL5	453
SMIM12	TSPYL6	Q8N831	447
SMIM12	KRT36	O76013	436
SMIM12	LEPROTL1	O95214	429

IntAct

23 interactions, top by confidence:

A	B	Type	Score
LAMP2	SMIM12	psi-mi:“MI:0915”(physical association)	0.560
SH3GLB1	SMIM12	psi-mi:“MI:0915”(physical association)	0.560
PRPF40A	SMIM12	psi-mi:“MI:0915”(physical association)	0.560
USB1	TOMM5	psi-mi:“MI:0914”(association)	0.350
SMIM12	VRK1	psi-mi:“MI:0914”(association)	0.350
	AP3B1	psi-mi:“MI:0914”(association)	0.350
LETM1	LETM2	psi-mi:“MI:0914”(association)	0.350
AIFM1	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
COX14	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
COX4I1	HAX1	psi-mi:“MI:2364”(proximity)	0.270
SCO1	HAX1	psi-mi:“MI:2364”(proximity)	0.270
SFXN1	HAX1	psi-mi:“MI:2364”(proximity)	0.270
IMMP1L	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
OMA1	HAX1	psi-mi:“MI:2364”(proximity)	0.270
PARL	HAX1	psi-mi:“MI:2364”(proximity)	0.270
	SMIM12	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (46): SMIM12 (Affinity Capture-MS), IL36A (Affinity Capture-MS), VRK1 (Affinity Capture-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS), SMIM12 (Proximity Label-MS)

ESM2 similar proteins: A1L2P2, A1XQT2, A5PJ82, A8MTT3, D2H617, D4ACP2, E2R5I0, F6USH3, G1QDE8, G1S9B8, O95139, P04038, P09669, P0CB93, P0CB94, P11951, P80977, Q02367, Q0MQ88, Q0MQ89, Q0MQ90, Q0MQE0, Q0MQE1, Q0Q4Z0, Q28EM2, Q28GF4, Q29259, Q3UIU2, Q4I8P5, Q5BKW8, Q5RK28, Q68EV8, Q78RX3, Q7YRJ8, Q7YRJ9, Q7YRK0, Q7YRK1, Q7YRK2, Q7YRK3, Q7YRK7

Diamond homologs: A1L2P2, A5PJ82, D2H617, D4ACP2, E2R5I0, F6USH3, G1QDE8, G1S9B8, Q28EM2, Q5BKW8, Q68EV8, Q78RX3, Q96EX1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1306 predictions. Top by Δscore:

Variant	Effect	Δscore
1:34755193:CAGG:C	donor_loss	1.0000
1:34755195:GGTAA:G	donor_loss	1.0000
1:34755196:G:GA	donor_loss	1.0000
1:34757302:TGCA:T	acceptor_loss	1.0000
1:34757303:GCA:G	acceptor_loss	1.0000
1:34757305:A:AG	acceptor_gain	1.0000
1:34757305:AGTA:A	acceptor_loss	1.0000
1:34757306:G:A	acceptor_loss	1.0000
1:34757306:G:GA	acceptor_gain	1.0000
1:34757306:GT:G	acceptor_gain	1.0000
1:34757306:GTA:G	acceptor_gain	1.0000
1:34757306:GTAGC:G	acceptor_gain	1.0000
1:34784727:A:AG	acceptor_gain	1.0000
1:34784728:A:G	acceptor_gain	1.0000
1:34784737:GGTA:G	acceptor_gain	1.0000
1:34794191:TTGCA:T	acceptor_loss	1.0000
1:34794192:TGCAG:T	acceptor_loss	1.0000
1:34794193:GCA:G	acceptor_loss	1.0000
1:34794194:CAGAC:C	acceptor_loss	1.0000
1:34794195:A:AG	acceptor_gain	1.0000
1:34794195:AGAC:A	acceptor_gain	1.0000
1:34794195:AGACG:A	acceptor_gain	1.0000
1:34794196:G:GA	acceptor_gain	1.0000
1:34794196:GAC:G	acceptor_gain	1.0000
1:34794196:GACG:G	acceptor_gain	1.0000
1:34794196:GACGG:G	acceptor_gain	1.0000
1:34855979:ACATC:A	acceptor_loss	1.0000
1:34855980:CAT:C	acceptor_gain	1.0000
1:34855980:CATCT:C	acceptor_loss	1.0000
1:34855981:ATC:A	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000140165 (1:34857806 TG>T), RS1000298447 (1:34858272 G>A,C), RS1000412452 (1:34857981 C>G,T), RS1000492477 (1:34858069 CA>C), RS1000653466 (1:34853401 G>A), RS1001088871 (1:34859481 T>C), RS1001562824 (1:34859170 G>A,T), RS1001827638 (1:34852809 G>A,T), RS1002110504 (1:34853046 C>T), RS1002365309 (1:34858479 G>A), RS1002402381 (1:34858812 C>T), RS1002504611 (1:34856421 G>A), RS1002511145 (1:34850255 T>C), RS1002553149 (1:34849881 G>A), RS1002664294 (1:34856154 C>A,G,T)

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

4 associations (top):

Study	Trait	p-value
GCST009612_3	Triglyceride levels x thiazide or thiazide-like diuretics use interaction	6.000000e-07
GCST90002400_23	Plateletcrit	3.000000e-11
GCST90002401_12	Platelet distribution width	1.000000e-22
GCST90002401_13	Platelet distribution width	3.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement
EFO:0007985	platelet crit
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, decreases methylation, decreases expression	2
Valproic Acid	increases expression, affects expression	2
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
di-n-butylphosphoric acid	affects expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	increases expression	1
Lead	affects expression	1
Methotrexate	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Silver	decreases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D8AY	Ubigene A-549 SMIM12 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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