SMIM7

Summary

SMIM7 (small integral membrane protein 7, HGNC:28419) is a protein-coding gene on chromosome 19p13.11, encoding Small integral membrane protein 7 (Q9BQ49).

Predicted to be located in membrane.

Source: NCBI Gene 79086 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_024104

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28419
Approved symbol	SMIM7
Name	small integral membrane protein 7
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC2747
Ensembl gene	ENSG00000214046
Ensembl biotype	protein_coding
Entrez	79086

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 13 nonsense_mediated_decay, 8 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000358726, ENST00000397349, ENST00000461364, ENST00000461488, ENST00000463051, ENST00000465250, ENST00000481671, ENST00000487416, ENST00000487803, ENST00000593404, ENST00000593409, ENST00000594507, ENST00000594662, ENST00000597711, ENST00000597781, ENST00000598278, ENST00000599310, ENST00000599872, ENST00000600740, ENST00000602194, ENST00000627144, ENST00000894889, ENST00000894890, ENST00000894891, ENST00000950147

RefSeq mRNA: 2 — MANE Select: NM_024104 NM_001300925, NM_024104

CCDS: CCDS12348, CCDS74307

Canonical transcript exons

ENST00000487416 — 5 exons

Exon	Start	End
ENSE00001861532	16646148	16647261
ENSE00003520062	16654035	16654125
ENSE00003562767	16659395	16659447
ENSE00003611124	16659959	16660000
ENSE00003631897	16660085	16660144

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 97.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 64.5325 / max 481.4799, expressed in 1825 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179826	64.5325	1825

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	97.08	gold quality
body of pancreas	UBERON:0001150	96.88	gold quality
pancreas	UBERON:0001264	96.57	gold quality
parotid gland	UBERON:0001831	96.46	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.43	gold quality
right adrenal gland	UBERON:0001233	96.09	gold quality
right adrenal gland cortex	UBERON:0035827	96.00	gold quality
rectum	UBERON:0001052	95.98	gold quality
body of stomach	UBERON:0001161	95.90	gold quality
left coronary artery	UBERON:0001626	95.88	gold quality
spinal cord	UBERON:0002240	95.87	gold quality
descending thoracic aorta	UBERON:0002345	95.85	gold quality
prostate gland	UBERON:0002367	95.83	gold quality
mucosa of transverse colon	UBERON:0004991	95.73	gold quality
coronary artery	UBERON:0001621	95.72	gold quality
ventricular zone	UBERON:0003053	95.72	gold quality
monocyte	CL:0000576	95.70	gold quality
left adrenal gland	UBERON:0001234	95.69	gold quality
left ovary	UBERON:0002119	95.62	gold quality
endocervix	UBERON:0000458	95.59	gold quality
smooth muscle tissue	UBERON:0001135	95.59	gold quality
thoracic aorta	UBERON:0001515	95.59	gold quality
mononuclear cell	CL:0000842	95.55	gold quality
left lobe of thyroid gland	UBERON:0001120	95.54	gold quality
ascending aorta	UBERON:0001496	95.54	gold quality
body of uterus	UBERON:0009853	95.54	gold quality
adrenal gland	UBERON:0002369	95.52	gold quality
right lobe of thyroid gland	UBERON:0001119	95.49	gold quality
peritoneum	UBERON:0002358	95.49	gold quality
omental fat pad	UBERON:0010414	95.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7303	no	384.60
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF

miRNA regulators (miRDB)

63 targeting SMIM7, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-4999-5P	99.35	69.15	926

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim7	ENSDARG00000074848
mus_musculus	Smim7	ENSMUSG00000044600
rattus_norvegicus	Smim7	ENSRNOG00000042037
caenorhabditis_elegans		WBGENE00302984

Protein

Protein identifiers

Small integral membrane protein 7 — Q9BQ49 (reviewed: Q9BQ49)

All UniProt accessions (6): B7WNH4, E9PLH2, E9PNA8, E9PP42, Q9BQ49, M0R0R3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SMIM7 family.

RefSeq proteins (2): NP_001287854, NP_077009* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037659	SMIM7	Family

UniProt features (5 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQ49-F1	66.05	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 131 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, CUI_TCF21_TARGETS_2_DN, NUYTTEN_EZH2_TARGETS_DN, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, chr19p13, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP, RATTENBACHER_BOUND_BY_CELF1, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, ASH1L_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

592 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM7	TMEM38A	Q9H6F2	669
SMIM7	CIMAP1D	Q3SX64	582
SMIM7	ANKRD13C	Q8N6S4	499
SMIM7	TMEM154	Q6P9G4	478
SMIM7	ZNF587B	E7ETH6	477
SMIM7	GABPB2	Q8TAK5	470
SMIM7	SPAG7	O75391	444
SMIM7	SYTL3	Q4VX76	419
SMIM7	FASTKD3	Q14CZ7	409
SMIM7	TYW3	Q6IPR3	408
SMIM7	TRAPPC1	Q9Y5R8	400
SMIM7	SSUH2	Q9Y2M2	399
SMIM7	MGAT4C	Q9UBM8	399
SMIM7	ZSCAN16	Q9H4T2	396
SMIM7	MFSD1	Q9H3U5	377

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SMIM7	DRD2	psi-mi:“MI:0915”(physical association)	0.370
SMIM7	CHRM4	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (4): SMIM7 (Two-hybrid), SMIM7 (Two-hybrid), SMIM7 (Affinity Capture-MS), SMIM7 (Affinity Capture-RNA)

ESM2 similar proteins: A4ZUA8, A4ZUA9, A4ZUC8, M1L4Z5, O31933, O55746, O66414, O96808, P05139, P07076, P07613, P0C2H1, P0CAM0, P0CAM1, P0CAM2, P0CAM3, P0DOM9, P0DON0, P15900, P15901, P19347, P20843, P30395, P31591, P42537, P48273, P49532, P51329, Q1XDF7, Q4VKV4, Q52PA5, Q58404, Q5RKS2, Q65176, Q6G607, Q6GDD7, Q6P317, Q70LB3, Q76RD1, Q76TT7

Diamond homologs: A5PLC9, B0BN70, B7QIN3, Q2KKX7, Q3SZ97, Q5RKS2, Q68F00, Q6INP0, Q6P317, Q9BQ49

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

632 predictions. Top by Δscore:

Variant	Effect	Δscore
19:16654027:GGACT:G	donor_loss	1.0000
19:16654028:GACTC:G	donor_loss	1.0000
19:16654029:ACTCA:A	donor_loss	1.0000
19:16654030:CTCAC:C	donor_loss	1.0000
19:16654032:CACA:C	donor_loss	1.0000
19:16654033:A:AC	donor_gain	1.0000
19:16654033:ACAC:A	donor_loss	1.0000
19:16654034:C:CA	donor_loss	1.0000
19:16654034:C:CC	donor_gain	1.0000
19:16654034:CA:C	donor_gain	1.0000
19:16654034:CACA:C	donor_gain	1.0000
19:16654034:CACAA:C	donor_gain	1.0000
19:16654125:CCT:C	acceptor_loss	1.0000
19:16654126:CTGGA:C	acceptor_loss	1.0000
19:16654127:T:A	acceptor_loss	1.0000
19:16659953:A:AC	donor_gain	1.0000
19:16659954:C:CC	donor_gain	1.0000
19:16659957:A:AC	donor_gain	1.0000
19:16659958:C:CC	donor_gain	1.0000
19:16659958:CAG:C	donor_gain	1.0000
19:16647258:CAGC:C	acceptor_gain	0.9900
19:16654026:TGGAC:T	donor_loss	0.9900
19:16654123:CAC:C	acceptor_gain	0.9900
19:16654126:C:CC	acceptor_gain	0.9900
19:16659954:CTCA:C	donor_gain	0.9900
19:16660081:TTA:T	donor_loss	0.9900
19:16660082:TAC:T	donor_loss	0.9900
19:16660083:A:AC	donor_gain	0.9900
19:16660083:AC:A	donor_gain	0.9900
19:16660084:C:CC	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000135279 (19:16662033 C>G,T), RS1000246092 (19:16656606 A>T), RS1000395429 (19:16650839 G>C), RS1000402060 (19:16661759 G>A), RS1000414602 (19:16645363 C>G,T), RS1000529241 (19:16657621 A>G), RS1000580179 (19:16658033 T>C), RS1000598728 (19:16651906 C>T), RS1000667317 (19:16650547 C>G), RS1000749390 (19:16646825 T>C), RS1000857174 (19:16641394 G>A), RS1000893613 (19:16647116 C>A), RS1000973842 (19:16635602 C>A), RS1001172792 (19:16635154 G>C), RS1001308660 (19:16635507 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, increases expression, affects cotreatment	6
sodium arsenite	affects expression, increases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases oxidation, increases abundance	1
bisphenol A	affects cotreatment, increases expression	1
arsenite	affects binding, increases reaction	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment, increases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	decreases expression	1
pentabromodiphenyl ether	increases expression	1
monomethylarsonous acid	decreases expression	1
pinostrobin	increases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, 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	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases expression, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases expression, increases oxidation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	affects expression	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects splicing	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, increases expression, increases oxidation, increases abundance	1

Clinical trials (associated diseases)

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