SMIM13

Summary

SMIM13 (small integral membrane protein 13, HGNC:27356) is a protein-coding gene on chromosome 6p24.2, encoding Small integral membrane protein 13 (P0DJ93).

Predicted to be located in membrane.

Source: NCBI Gene 221710 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001135575

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27356
Approved symbol	SMIM13
Name	small integral membrane protein 13
Location	6p24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000224531
Ensembl biotype	protein_coding
Entrez	221710

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000376935, ENST00000416247, ENST00000716083

RefSeq mRNA: 1 — MANE Select: NM_001135575 NM_001135575

CCDS: CCDS56396

Canonical transcript exons

ENST00000416247 — 2 exons

Exon	Start	End
ENSE00001593326	11093834	11094389
ENSE00004028797	11134403	11138733

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 98.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.6631 / max 434.1932, expressed in 1802 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
65789	11.3617	1774
65790	5.3181	1665
65791	0.4937	286
65792	0.4896	96

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	98.97	gold quality
middle temporal gyrus	UBERON:0002771	98.66	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.29	gold quality
postcentral gyrus	UBERON:0002581	97.85	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.85	gold quality
Brodmann (1909) area 46	UBERON:0006483	97.85	gold quality
pons	UBERON:0000988	97.84	gold quality
endothelial cell	CL:0000115	97.40	gold quality
parietal lobe	UBERON:0001872	97.32	gold quality
superior frontal gyrus	UBERON:0002661	96.69	gold quality
dorsal plus ventral thalamus	UBERON:0001897	96.56	gold quality
superior vestibular nucleus	UBERON:0007227	96.29	gold quality
substantia nigra pars compacta	UBERON:0001965	96.21	gold quality
subthalamic nucleus	UBERON:0001906	96.03	gold quality
entorhinal cortex	UBERON:0002728	95.98	gold quality
medulla oblongata	UBERON:0001896	95.82	gold quality
cortical plate	UBERON:0005343	95.66	gold quality
substantia nigra pars reticulata	UBERON:0001966	95.57	gold quality
inferior vagus X ganglion	UBERON:0005363	95.19	gold quality
occipital lobe	UBERON:0002021	95.02	gold quality
deltoid	UBERON:0001476	94.62	gold quality
primary visual cortex	UBERON:0002436	94.44	gold quality
tibialis anterior	UBERON:0001385	94.19	gold quality
globus pallidus	UBERON:0001875	93.92	gold quality
lateral globus pallidus	UBERON:0002476	93.78	gold quality
medial globus pallidus	UBERON:0002477	93.65	gold quality
left ventricle myocardium	UBERON:0006566	93.12	gold quality
biceps brachii	UBERON:0001507	93.11	gold quality
ventral tegmental area	UBERON:0002691	93.01	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	92.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

252 targeting SMIM13, 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-4668-3P	100.00	68.74	2635
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim13	ENSDARG00000089204
mus_musculus	Smim13	ENSMUSG00000091264
rattus_norvegicus	Smim13	ENSRNOG00000073728
rattus_norvegicus		ENSRNOG00000076559

Protein

Protein identifiers

Small integral membrane protein 13 — P0DJ93 (reviewed: P0DJ93)

All UniProt accessions (1): P0DJ93

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SMIM13 family.

RefSeq proteins (1): NP_001129047* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031851	DUF4750	Family

Pfam: PF15938

UniProt features (9 total): modified residue 4, compositionally biased region 2, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DJ93-F1	69.34	0.18

Functional residue map

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

Post-translational modifications (4): 58, 60, 62, 69

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): chr6p24, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, JOHNSTONE_PARVB_TARGETS_2_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, LIM_MAMMARY_STEM_CELL_UP, DIDO1_TARGET_GENES, FEV_TARGET_GENES, HHEX_TARGET_GENES, HMG20B_TARGET_GENES, NFE2L1_TARGET_GENES, SFMBT1_TARGET_GENES, TAFAZZIN_TARGET_GENES, ZNF175_TARGET_GENES, ZNF2_TARGET_GENES

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

526 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM13	C11orf24	Q96F05	479
SMIM13	CNIH4	Q9P003	465
SMIM13	FAM110A	Q9BQ89	447
SMIM13	TIGD2	Q4W5G0	428
SMIM13	TMEM72	A0PK05	394
SMIM13	TMED3	Q9Y3Q3	374
SMIM13	TMED9	Q9BVK6	365
SMIM13	TAFA1	Q7Z5A9	362
SMIM13	AVL9	Q8NBF6	359
SMIM13	SNX29	Q8TEQ0	354
SMIM13	SRP68	Q9UHB9	333
SMIM13	SLC12A2	P55011	332
SMIM13	DCLK2	Q8N568	326
SMIM13	WBP11	Q9Y2W2	325
SMIM13	GPR180	Q86V85	325

IntAct

0 interactions, top by confidence:

BioGRID (2): SMIM13 (Affinity Capture-RNA), SMIM13 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSN8, A0A1B0GSZ0, A0A1B0GVQ0, A0A1B0GVT2, A0A1B0GWG4, A2A2V5, A2A9G7, A2APA5, A2VE22, A6NFZ4, A6QQ93, A7E1Z1, A7MB05, A9CBA0, B7ZWI3, D3ZR35, E9Q942, F5HAK6, F5HFG3, O14668, O39519, O39920, P09312, P0DJ93, P18345, P86045, Q2KIK3, Q498C7, Q5RCB6, Q5RF07, Q5RF75, Q67593, Q68D42, Q6AXS2, Q6UWT2, Q77NN6, Q7M750, Q80WK2, Q8BGN6

Diamond homologs: B8JJV5, D3ZR35, E9Q942, P0DJ93

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

892 predictions. Top by Δscore:

Variant	Effect	Δscore
6:11094385:GTGCG:G	donor_gain	1.0000
6:11134401:AGGTT:A	acceptor_gain	1.0000
6:11134402:GGTTG:G	acceptor_gain	1.0000
6:11094387:GCG:G	donor_gain	0.9900
6:11094390:G:GA	donor_loss	0.9900
6:11094390:G:GG	donor_gain	0.9900
6:11094391:TGA:T	donor_loss	0.9900
6:11094392:GA:G	donor_loss	0.9900
6:11094806:AG:A	donor_gain	0.9900
6:11134399:GTAG:G	acceptor_loss	0.9900
6:11134400:TA:T	acceptor_loss	0.9900
6:11134402:G:GT	acceptor_loss	0.9900
6:11134402:GGTT:G	acceptor_gain	0.9900
6:11094393:AG:A	donor_loss	0.9800
6:11105477:T:C	donor_gain	0.9800
6:11111310:A:C	acceptor_gain	0.9800
6:11111676:CCA:C	donor_gain	0.9800
6:11134402:GGT:G	acceptor_gain	0.9800
6:11105476:AT:A	donor_gain	0.9700
6:11111625:A:AC	donor_gain	0.9700
6:11111626:C:CC	donor_gain	0.9700
6:11119715:A:AG	acceptor_gain	0.9700
6:11119716:G:GG	acceptor_gain	0.9700
6:11134401:A:AG	acceptor_gain	0.9700
6:11134401:AG:A	acceptor_gain	0.9700
6:11134402:G:GG	acceptor_gain	0.9700
6:11134402:GG:G	acceptor_gain	0.9700
6:11094805:TA:T	donor_gain	0.9600
6:11103759:TGGC:T	acceptor_gain	0.9600
6:11111301:T:TC	acceptor_gain	0.9600

AlphaMissense

574 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:11134438:T:C	F38L	0.998
6:11134440:C:A	F38L	0.998
6:11134440:C:G	F38L	0.998
6:11134405:T:A	W27R	0.996
6:11134405:T:C	W27R	0.996
6:11134445:T:C	F40S	0.996
6:11134417:T:A	W31R	0.995
6:11134417:T:C	W31R	0.995
6:11134448:T:A	L41H	0.995
6:11134439:T:C	F38S	0.994
6:11134426:T:C	F34L	0.993
6:11134428:T:A	F34L	0.993
6:11134428:T:G	F34L	0.993
6:11134445:T:G	F40C	0.993
6:11094389:G:C	G26R	0.992
6:11134438:T:A	F38I	0.991
6:11134427:T:C	F34S	0.989
6:11134444:T:C	F40L	0.989
6:11134446:T:A	F40L	0.989
6:11134446:T:G	F40L	0.989
6:11134419:G:C	W31C	0.988
6:11134419:G:T	W31C	0.988
6:11134430:T:C	L35S	0.988
6:11134439:T:G	F38C	0.988
6:11134457:T:C	L44P	0.988
6:11134424:T:C	L33P	0.987
6:11134438:T:G	F38V	0.987
6:11134448:T:C	L41P	0.987
6:11134403:G:A	G26D	0.984
6:11134436:A:T	K37I	0.984

dbSNP variants (sampled 300 via entrez): RS1000019683 (6:11105671 A>G), RS1000088105 (6:11104046 A>T), RS1000089314 (6:11131760 A>G), RS1000160074 (6:11133294 A>G), RS1000209663 (6:11102869 A>G), RS1000271408 (6:11131485 A>C,G), RS1000332550 (6:11133800 T>C), RS1000356304 (6:11117638 A>G), RS1000392705 (6:11137747 A>G), RS1000447130 (6:11133676 A>C), RS1000449088 (6:11094250 C>A,T), RS1000454643 (6:11105282 A>G), RS1000465887 (6:11101041 T>C), RS1000620017 (6:11107651 C>G), RS1000678837 (6:11109225 C>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

2 associations (top):

Study	Trait	p-value
GCST002579_16	Heschl’s gyrus morphology	3.000000e-06
GCST003098_31	Diabetic kidney disease	9.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression	3
sodium arsenite	increases abundance, increases expression	2
Cyclosporine	increases expression	2
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	increases abundance, increases expression	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
jinfukang	decreases expression	1
PCI 5002	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	increases abundance, increases expression	1
Cisplatin	increases expression	1
Lead	affects expression	1
Manganese	increases abundance, increases expression	1
Silver	increases expression	1
Dihydrotestosterone	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Oxyquinoline	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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