SMIM2

Summary

SMIM2 (small integral membrane protein 2, HGNC:28776) is a protein-coding gene on chromosome 13q14.11, encoding Small integral membrane protein 2 (Q9BVW6).

Predicted to be located in membrane.

Source: NCBI Gene 79024 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 1 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28776
Approved symbol	SMIM2
Name	small integral membrane protein 2
Location	13q14.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC5590
Ensembl gene	ENSG00000139656
Entrez	79024

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 90.55.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	90.55	gold quality
right testis	UBERON:0004534	90.23	gold quality
testis	UBERON:0000473	85.71	gold quality
sperm	CL:0000019	77.29	gold quality
male germ cell	CL:0000015	75.05	gold quality
buccal mucosa cell	CL:0002336	68.18	gold quality
right coronary artery	UBERON:0001625	58.45	gold quality
mucosa of stomach	UBERON:0001199	58.03	gold quality
smooth muscle tissue	UBERON:0001135	55.06	gold quality
pancreatic ductal cell	CL:0002079	54.11	silver quality
popliteal artery	UBERON:0002250	53.77	gold quality
tibial artery	UBERON:0007610	53.76	gold quality
islet of Langerhans	UBERON:0000006	53.25	gold quality
cartilage tissue	UBERON:0002418	52.92	gold quality
rectum	UBERON:0001052	52.37	gold quality
small intestine Peyer’s patch	UBERON:0003454	52.09	gold quality
transverse colon	UBERON:0001157	51.36	gold quality
adult mammalian kidney	UBERON:0000082	50.95	gold quality
metanephros cortex	UBERON:0010533	50.69	gold quality
metanephros	UBERON:0000081	50.41	gold quality
epithelial cell of pancreas	CL:0000083	50.18	gold quality
small intestine	UBERON:0002108	49.73	gold quality
coronary artery	UBERON:0001621	49.41	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
left coronary artery	UBERON:0001626	49.18	gold quality
hair follicle	UBERON:0002073	49.18	gold quality
muscle tissue	UBERON:0002385	49.17	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.79

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Small integral membrane protein 2 — Q9BVW6 (reviewed: Q9BVW6)

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BVW6-F1	67.00	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

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

78 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM2	SMIM1	B2RUZ4	446
SMIM2	SMIM3	Q9BZL3	418
SMIM2	GAL3ST4	Q96RP7	400
SMIM2	UBXN11	Q5T124	370
SMIM2	MACIR	Q96GV9	366
SMIM2	INTS1	Q8N201	366
SMIM2	DNAAF5	Q86Y56	348
SMIM2	ANKRD55	Q3KP44	317
SMIM2	CLYBL	Q8N0X4	317
SMIM2	BBX	Q8WY36	307
SMIM2	RAI14	Q9P0K7	303
SMIM2	BLCAP	P62952	271
SMIM2	RNASET2	O00584	260
SMIM2	ST3GAL3	Q11203	257
SMIM2	ST3GAL6	Q9Y274	257

IntAct

10 interactions, top by confidence:

A	B	Type	Score
UBQLN1	SMIM2	psi-mi:“MI:0915”(physical association)	0.560
SMIM2	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
SMIM2	UBQLN2	psi-mi:“MI:0915”(physical association)	0.560
SMIM2	UBQLN2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): SMIM2 (Two-hybrid), UBQLN2 (Two-hybrid)

ESM2 similar proteins: A0A1B0GUQ0, A0A1B0GV22, A4WGH3, A5WBB8, A8A6G6, B1IX34, B1X9T3, B5BIL7, B5QUQ3, B5RFY4, B7L848, B7LK47, B7M557, B7MGC6, B7N2F0, B7NF22, B7NR07, B8MYS5, C0Q2L2, C4ZYY2, O71190, O83770, P03167, P03168, P05443, P0A8C8, P0A8C9, P0C304, P0C305, P12173, P12478, P20464, P53231, P61468, P61472, Q16612, Q1R4N0, Q31UV8, Q329B3, Q3SSW2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1 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

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000076053 (13:44162683 C>T), RS1000232448 (13:44162319 A>T), RS1000463019 (13:44155442 T>C), RS1000797890 (13:44150470 C>A,G), RS1000829921 (13:44159899 C>G), RS1000897021 (13:44160362 C>G,T), RS1001007641 (13:44152635 T>A), RS1001062158 (13:44145427 A>G), RS1001234251 (13:44162175 G>T), RS1001350159 (13:44157266 C>T), RS1001737581 (13:44159479 C>A), RS1002011720 (13:44150053 C>T), RS1002127726 (13:44149733 C>T), RS1002379611 (13:44146691 C>T), RS1002632758 (13:44153427 G>A,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

5 associations (top):

Study	Trait	p-value
GCST004505_105	Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)	1.000000e-08
GCST004508_26	Waist-to-hip ratio adjusted for BMI in non-smokers	3.000000e-10
GCST004858_16	Dupuytren’s disease	2.000000e-10
GCST007401_20	Factor VII activity	2.000000e-06
GCST011769_5	Schizophrenia	1.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004318	smoking behavior
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0004229	Dupuytren Contracture
EFO:0004619	factor VII measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
sodium arsenite	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
Cadmium	increases abundance, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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