SMIM18

Summary

SMIM18 (small integral membrane protein 18, HGNC:42973) is a protein-coding gene on chromosome 8p12, encoding Small integral membrane protein 18 (P0DKX4).

Predicted to be located in membrane.

Source: NCBI Gene 100507341 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001206847

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:42973
Approved symbol	SMIM18
Name	small integral membrane protein 18
Location	8p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000253457
Ensembl biotype	protein_coding
Entrez	100507341

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000517349, ENST00000943662

RefSeq mRNA: 1 — MANE Select: NM_001206847 NM_001206847

CCDS: CCDS56529

Canonical transcript exons

ENST00000517349 — 3 exons

Exon	Start	End
ENSE00002090575	30644492	30644572
ENSE00002109197	30638580	30638639
ENSE00002139359	30645281	30646064

Expression profiles

Bgee: expression breadth broad, 95 present calls, max score 86.22.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.1265 / max 58.1901, expressed in 156 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
88324	1.1265	156

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	86.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.95	silver quality
ganglionic eminence	UBERON:0004023	80.99	gold quality
hypothalamus	UBERON:0001898	79.99	gold quality
cerebellar cortex	UBERON:0002129	77.56	gold quality
cerebellar hemisphere	UBERON:0002245	77.52	gold quality
cerebellum	UBERON:0002037	77.39	gold quality
right hemisphere of cerebellum	UBERON:0014890	76.87	gold quality
prefrontal cortex	UBERON:0000451	76.82	gold quality
frontal cortex	UBERON:0001870	74.40	gold quality
superior frontal gyrus	UBERON:0002661	74.36	gold quality
cerebral cortex	UBERON:0000956	73.60	gold quality
pituitary gland	UBERON:0000007	73.46	gold quality
Ammon’s horn	UBERON:0001954	73.44	gold quality
brain	UBERON:0000955	73.19	gold quality
anterior cingulate cortex	UBERON:0009835	72.93	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.86	gold quality
Brodmann (1909) area 9	UBERON:0013540	72.53	gold quality
substantia nigra	UBERON:0002038	72.49	gold quality
amygdala	UBERON:0001876	72.34	gold quality
temporal lobe	UBERON:0001871	71.67	gold quality
nucleus accumbens	UBERON:0001882	71.55	gold quality
right frontal lobe	UBERON:0002810	71.50	gold quality
adenohypophysis	UBERON:0002196	71.40	gold quality
islet of Langerhans	UBERON:0000006	70.73	gold quality
primary visual cortex	UBERON:0002436	70.39	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	69.54	gold quality
putamen	UBERON:0001874	68.57	gold quality
caudate nucleus	UBERON:0001873	66.74	gold quality
ventricular zone	UBERON:0003053	63.76	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting SMIM18, 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-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-3127-3P	98.94	67.34	1055
HSA-MIR-6756-3P	98.94	66.79	1104
HSA-MIR-1183	98.75	67.10	1116
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-558	97.50	67.16	977
HSA-MIR-3059-3P	96.71	67.08	606
HSA-MIR-4680-5P	96.43	67.15	893

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim18	ENSDARG00000093064
mus_musculus	Smim18	ENSMUSG00000094500
rattus_norvegicus	Smim18	ENSRNOG00000049689

Protein

Protein identifiers

Small integral membrane protein 18 — P0DKX4 (reviewed: P0DKX4)

All UniProt accessions (1): P0DKX4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001193776* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031671	SMIM5/18/22	Family
IPR053081	SIM_Modulators	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-P0DKX4-F1	71.20	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): chr8p12, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, MIR4756_3P, MIR6878_3P, MANNO_MIDBRAIN_NEUROTYPES_HNBM, MANNO_MIDBRAIN_NEUROTYPES_HNBML1, MANNO_MIDBRAIN_NEUROTYPES_HRN, MANNO_MIDBRAIN_NEUROTYPES_HDA, MANNO_MIDBRAIN_NEUROTYPES_HDA2, MANNO_MIDBRAIN_NEUROTYPES_HNBGABA, MANNO_MIDBRAIN_NEUROTYPES_HSERT, HU_FETAL_RETINA_RGC, DESCARTES_FETAL_ADRENAL_CSH1_CSH2_POSITIVE_CELLS, HE_LIM_SUN_FETAL_LUNG_C7_SST_POS_NEURON_CELL, HE_LIM_SUN_FETAL_LUNG_C7_TM4SF4_POS_PENK_POS_NEURON_CELL

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

38 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM18	ABRACL	Q9P1F3	555
SMIM18	NOVA2	Q9UNW9	388
SMIM18	BARX1	Q9HBU1	370
SMIM18	RGS16	O15492	360
SMIM18	ETV1	P50549	239
SMIM18	MEIS3	Q99687	224
SMIM18	TFAP2E	Q6VUC0	220
SMIM18	TNNC2	P02585	184
SMIM18	SOX10	P56693	182
SMIM18	GNG2	P59768	181
SMIM18	SLC6A5	Q9Y345	181
SMIM18	STX1B	P61266	167
SMIM18	MEOX1	P50221	167
SMIM18	TFEC	O14948	165
SMIM18	LMO1	P25800	153

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GQX3, A0A1B0GRQ0, A0A1B0GV90, A4D0T7, A4QNL6, A6NFZ4, A9RA88, B0CMA4, B3DHH5, C0HJJ0, C1PGW0, D3YUK8, F2Z3Y9, F5HFG3, G1TZA0, G2TRP0, O13001, O14068, O39920, P0DKX4, P34535, P57054, P61807, P61808, Q06FW7, Q19443, Q3E8L0, Q3E912, Q3T0S0, Q4V921, Q54L98, Q5F3W2, Q5R687, Q5RBD8, Q5U4Q2, Q66J27, Q6PQZ3, Q80UA9, Q80ZU4, Q8AUU1

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

419 predictions. Top by Δscore:

Variant	Effect	Δscore
8:30644486:A:AG	acceptor_gain	1.0000
8:30645363:TTTTC:T	donor_gain	1.0000
8:30638637:GAG:G	donor_gain	0.9900
8:30638638:AGG:A	donor_loss	0.9900
8:30638640:G:GG	donor_gain	0.9900
8:30644487:C:G	acceptor_gain	0.9900
8:30644508:A:AG	acceptor_gain	0.9900
8:30644509:G:GG	acceptor_gain	0.9900
8:30644569:AAAGG:A	donor_loss	0.9900
8:30644570:AAGG:A	donor_loss	0.9900
8:30644571:AGGTA:A	donor_loss	0.9900
8:30644573:G:A	donor_loss	0.9900
8:30644574:T:G	donor_loss	0.9900
8:30645279:A:AG	acceptor_gain	0.9900
8:30645280:G:GG	acceptor_gain	0.9900
8:30645278:TAG:T	acceptor_loss	0.9800
8:30645279:A:C	acceptor_loss	0.9800
8:30645280:G:C	acceptor_loss	0.9800
8:30645353:A:AG	donor_gain	0.9800
8:30645354:G:GG	donor_gain	0.9800
8:30642553:ATC:A	donor_gain	0.9700
8:30644491:GCCA:G	acceptor_gain	0.9700
8:30644503:GATTC:G	acceptor_loss	0.9700
8:30644504:ATTCA:A	acceptor_loss	0.9700
8:30644505:TTCAG:T	acceptor_loss	0.9700
8:30644506:TCAG:T	acceptor_loss	0.9700
8:30644507:CAGAT:C	acceptor_loss	0.9700
8:30644508:A:T	acceptor_loss	0.9700
8:30644509:G:GC	acceptor_loss	0.9700
8:30645444:A:AG	acceptor_gain	0.9700

AlphaMissense

633 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:30645402:G:C	W31C	0.997
8:30645402:G:T	W31C	0.997
8:30645400:T:A	W31R	0.995
8:30645400:T:C	W31R	0.995
8:30645455:T:C	L49S	0.995
8:30645410:C:A	A34D	0.993
8:30645412:T:C	C35R	0.992
8:30645437:T:A	I43K	0.992
8:30645443:C:A	T45K	0.992
8:30645433:T:C	F42L	0.991
8:30645435:T:A	F42L	0.991
8:30645435:T:G	F42L	0.991
8:30645434:T:C	F42S	0.990
8:30645467:C:A	A53D	0.989
8:30645419:T:A	V37D	0.988
8:30645422:T:A	I38N	0.986
8:30645464:T:G	L52R	0.986
8:30645464:T:C	L52P	0.985
8:30645425:T:G	L39R	0.984
8:30645437:T:G	I43R	0.984
8:30645464:T:A	L52Q	0.984
8:30645425:T:C	L39P	0.983
8:30645443:C:G	T45R	0.983
8:30645388:T:C	F27L	0.982
8:30645390:C:A	F27L	0.982
8:30645390:C:G	F27L	0.982
8:30645389:T:G	F27C	0.981
8:30645415:T:C	F36L	0.981
8:30645417:T:A	F36L	0.981
8:30645417:T:G	F36L	0.981

dbSNP variants (sampled 300 via entrez): RS1000259393 (8:30643713 T>C), RS1000315878 (8:30637129 T>C), RS1000347021 (8:30637323 G>C), RS1000543383 (8:30641657 A>C), RS1000544624 (8:30641601 C>A,T), RS1000592637 (8:30641930 G>C), RS1000609827 (8:30643338 A>C), RS1002116372 (8:30645908 A>T), RS1002170207 (8:30645659 A>G), RS1002266630 (8:30640724 G>A,T), RS1002309300 (8:30645297 G>A,T), RS1002559292 (8:30638863 A>G), RS1002571099 (8:30639197 A>C,T), RS1003043931 (8:30645196 A>G), RS1003431789 (8:30644028 A>AT)

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

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium	decreases expression, increases abundance	1
Rotenone	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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