SMIM15

Summary

SMIM15 (small integral membrane protein 15, HGNC:33861) is a protein-coding gene on chromosome 5q12.1, encoding Small integral membrane protein 15 (Q7Z3B0).

Predicted to be located in membrane.

Source: NCBI Gene 643155 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001048249

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33861
Approved symbol	SMIM15
Name	small integral membrane protein 15
Location	5q12.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP686E2158
Ensembl gene	ENSG00000188725
Ensembl biotype	protein_coding
Entrez	643155

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000339020, ENST00000507416, ENST00000893260, ENST00000893261, ENST00000893262, ENST00000893263, ENST00000893264, ENST00000951600, ENST00000951601, ENST00000951602, ENST00000951603

RefSeq mRNA: 1 — MANE Select: NM_001048249 NM_001048249

CCDS: CCDS34165

Canonical transcript exons

ENST00000339020 — 3 exons

Exon	Start	End
ENSE00001364025	61162217	61162468
ENSE00001365733	61157704	61160199
ENSE00001377754	61161088	61161227

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 98.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.7672 / max 265.9175, expressed in 1810 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
61906	24.7672	1810

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	98.65	gold quality
palpebral conjunctiva	UBERON:0001812	98.29	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.27	gold quality
colonic mucosa	UBERON:0000317	98.09	gold quality
jejunal mucosa	UBERON:0000399	97.40	gold quality
kidney epithelium	UBERON:0004819	97.01	gold quality
esophagus squamous epithelium	UBERON:0006920	96.81	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.66	gold quality
epithelium of nasopharynx	UBERON:0001951	96.21	gold quality
corpus epididymis	UBERON:0004359	96.15	gold quality
germinal epithelium of ovary	UBERON:0001304	95.98	gold quality
caput epididymis	UBERON:0004358	95.93	gold quality
upper arm skin	UBERON:0004263	95.69	gold quality
oral cavity	UBERON:0000167	95.66	gold quality
seminal vesicle	UBERON:0000998	95.50	gold quality
epithelial cell of pancreas	CL:0000083	95.39	gold quality
nasal cavity epithelium	UBERON:0005384	95.38	gold quality
bronchial epithelial cell	CL:0002328	95.19	gold quality
duodenum	UBERON:0002114	95.03	gold quality
gingiva	UBERON:0001828	94.96	gold quality
skin of hip	UBERON:0001554	94.94	gold quality
islet of Langerhans	UBERON:0000006	94.93	gold quality
bronchus	UBERON:0002185	94.88	gold quality
lower lobe of lung	UBERON:0008949	94.74	gold quality
upper leg skin	UBERON:0004262	94.55	gold quality
gingival epithelium	UBERON:0001949	94.45	gold quality
amniotic fluid	UBERON:0000173	94.27	gold quality
cauda epididymis	UBERON:0004360	94.24	gold quality
mammalian vulva	UBERON:0000997	94.10	gold quality
cartilage tissue	UBERON:0002418	94.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting SMIM15, 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-340-5P	100.00	72.50	4437
HSA-MIR-3134	100.00	66.43	777
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-186-5P	99.99	70.83	3707
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-4760-3P	99.93	70.50	2385

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim15	ENSMUSG00000071180
rattus_norvegicus	Smim15	ENSRNOG00000031995

Protein

Protein identifiers

Small integral membrane protein 15 — Q7Z3B0 (reviewed: Q7Z3B0)

All UniProt accessions (1): Q7Z3B0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SMIM15 family.

RefSeq proteins (1): NP_001041714* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027877	Smim15	Family

Pfam: PF15086

UniProt features (6 total): chain 1, transmembrane region 1, region of interest 1, coiled-coil region 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z3B0-F1	93.88	0.91

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): MILI_PSEUDOPODIA_HAPTOTAXIS_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, chr5q12, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_4_UP, FIGUEROA_AML_METHYLATION_CLUSTER_6_UP, FIGUEROA_AML_METHYLATION_CLUSTER_7_UP, PILON_KLF1_TARGETS_UP, JOHNSTONE_PARVB_TARGETS_3_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, YANG_BCL3_TARGETS_UP, DLX6_TARGET_GENES, DMRT1_TARGET_GENES, PHF21A_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

216 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM15	SREK1IP1	Q8N9Q2	623
SMIM15	SYS1	Q8N2H4	475
SMIM15	PRDM15	P57071	472
SMIM15	IFFO2	Q5TF58	447
SMIM15	TSPAN14	Q8NG11	447
SMIM15	RFX8	Q6ZV50	440
SMIM15	ARFRP1	Q13795	422
SMIM15	HSDL1	Q3SXM5	418
SMIM15	DIS3L2	Q8IYB7	413
SMIM15	ZNF354A	O60765	378
SMIM15	TUSC1	Q2TAM9	376
SMIM15	KRT85	P78386	370
SMIM15	DESI1	Q6ICB0	370
SMIM15	HOXD9	P28356	359
SMIM15	DESI2	Q9BSY9	359

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PBX4	SMIM15	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): PBX4 (Proximity Label-MS), SMIM15 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDV9, A3KNM5, A4II09, A4R0J5, A5PJ82, A9JTJ0, B8JLV7, D2H617, D4ACP2, E2R5I0, F6USH3, G1QDE8, G1S9B8, P14790, P42551, P42552, P42553, P42554, P56378, Q08013, Q28F39, Q28GR4, Q2M146, Q3B8H3, Q3SZ87, Q3UTD9, Q42337, Q4V7U1, Q58E26, Q5BK13, Q5F409, Q5R4D8, Q5RAS8, Q5RCY6, Q5REX0, Q5ZLL0, Q6DFS0, Q6IQC7, Q78RX3, Q7XLX6

Diamond homologs: A3KNM5, A9JTJ0, Q3UTD9, Q5F409, Q5R4D8, Q7Z3B0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

390 predictions. Top by Δscore:

Variant	Effect	Δscore
5:61161113:A:C	donor_gain	1.0000
5:61161224:TTGG:T	acceptor_gain	1.0000
5:61161228:C:CC	acceptor_gain	1.0000
5:61161232:T:C	acceptor_gain	1.0000
5:61161232:T:TC	acceptor_gain	1.0000
5:61160062:CTTG:C	acceptor_gain	0.9900
5:61160195:TGGGG:T	acceptor_gain	0.9900
5:61160200:C:CC	acceptor_gain	0.9900
5:61160210:CGGG:C	acceptor_gain	0.9900
5:61160211:G:T	acceptor_gain	0.9900
5:61160213:G:C	acceptor_gain	0.9900
5:61160213:G:GC	acceptor_gain	0.9900
5:61160221:C:CT	acceptor_gain	0.9900
5:61160223:C:CT	acceptor_gain	0.9900
5:61160224:A:T	acceptor_gain	0.9900
5:61161223:ATTGG:A	acceptor_gain	0.9900
5:61161225:TGG:T	acceptor_gain	0.9900
5:61161226:GG:G	acceptor_gain	0.9900
5:61161226:GGC:G	acceptor_loss	0.9900
5:61161228:C:T	acceptor_loss	0.9900
5:61161229:T:C	acceptor_loss	0.9900
5:61161241:A:AC	acceptor_gain	0.9900
5:61161241:A:C	acceptor_gain	0.9900
5:61160198:GGC:G	acceptor_loss	0.9800
5:61160199:GCT:G	acceptor_loss	0.9800
5:61160201:T:A	acceptor_loss	0.9800
5:61161083:TCTAC:T	donor_loss	0.9800
5:61161084:CTACC:C	donor_loss	0.9800
5:61161086:A:C	donor_loss	0.9800
5:61161088:C:G	donor_loss	0.9800

AlphaMissense

481 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:61160059:G:T	A38D	0.998
5:61160077:G:T	P32Q	0.998
5:61160128:G:T	A15D	0.998
5:61160077:G:C	P32R	0.997
5:61160083:A:T	L30H	0.997
5:61160106:G:C	F22L	0.997
5:61160106:G:T	F22L	0.997
5:61160107:A:G	F22S	0.997
5:61160108:A:G	F22L	0.997
5:61160071:A:G	F34S	0.996
5:61160095:A:T	V26D	0.996
5:61160041:A:G	L44S	0.995
5:61160061:A:C	S37R	0.995
5:61160061:A:T	S37R	0.995
5:61160063:T:G	S37R	0.995
5:61160065:G:T	A36E	0.995
5:61160068:A:C	L35R	0.995
5:61160086:G:T	A29D	0.994
5:61160126:C:G	A16P	0.994
5:61160068:A:T	L35Q	0.993
5:61160116:G:A	P19L	0.993
5:61160116:G:T	P19H	0.993
5:61160140:A:T	V11D	0.993
5:61160104:A:T	L23H	0.992
5:61160132:A:G	W14R	0.992
5:61160132:A:T	W14R	0.992
5:61160038:G:T	A45D	0.991
5:61160039:C:G	A45P	0.991
5:61160024:C:G	A50P	0.988
5:61160074:A:T	L33Q	0.988

dbSNP variants (sampled 300 via entrez): RS1000566152 (5:61162467 G>A,T), RS1000803777 (5:61164036 G>A), RS1000810771 (5:61159106 G>A), RS1000862998 (5:61158945 T>C), RS1001954485 (5:61161122 T>C), RS1002260159 (5:61157837 G>C), RS1002374732 (5:61158204 A>G), RS1002815956 (5:61162526 A>C), RS1002868408 (5:61162288 T>A), RS1004371733 (5:61157775 G>C,T), RS1004704939 (5:61159689 A>C), RS1004746412 (5:61162774 G>C), RS1005272031 (5:61163520 G>A), RS10056202 (5:61163578 G>A,T), RS1006760677 (5:61162637 G>C)

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

9 associations (top):

Study	Trait	p-value
GCST002149_22	Schizophrenia	4.000000e-08
GCST004521_137	Autism spectrum disorder or schizophrenia	2.000000e-09
GCST004521_26	Autism spectrum disorder or schizophrenia	1.000000e-09
GCST004521_260	Autism spectrum disorder or schizophrenia	6.000000e-09
GCST007327_87	Smoking status (ever vs never smokers)	6.000000e-10
GCST009391_1924	Metabolite levels	5.000000e-06
GCST010701_32	Cortical surface area (MOSTest)	2.000000e-29
GCST010702_115	Subcortical volume (MOSTest)	2.000000e-09
GCST010703_98	Brain morphology (MOSTest)	5.000000e-41

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004318	smoking behavior
EFO:0010464	beta-aminoisobutyric acid measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, increases abundance, increases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
arsenite	affects binding, increases reaction	1
di-n-butylphosphoric acid	affects expression	1
picoxystrobin	increases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Carbamazepine	affects expression	1
Ketoconazole	increases expression	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	affects expression	1
Vanadates	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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