SMIM30

Summary

SMIM30 (small integral membrane protein 30, HGNC:48953) is a protein-coding gene on chromosome 7q31.1, encoding Small integral membrane protein 30 (A4D0T7). Negatively regulates antiviral innate immune responses.

Involved in negative regulation of type I interferon-mediated signaling pathway. Located in endoplasmic reticulum membrane and mitochondrial membrane.

Source: NCBI Gene 401397 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001352688

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48953
Approved symbol	SMIM30
Name	small integral membrane protein 30
Location	7q31.1
Locus type	gene with protein product
Status	Approved
Aliases	MAVI1
Ensembl gene	ENSG00000214194
Ensembl biotype	protein_coding
Entrez	401397

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 retained_intron

ENST00000397764, ENST00000413744, ENST00000439551, ENST00000441359, ENST00000881812, ENST00000914302

RefSeq mRNA: 2 — MANE Select: NM_001352688 NM_001352687, NM_001352688

CCDS: CCDS87543

Canonical transcript exons

ENST00000397764 — 3 exons

Exon	Start	End
ENSE00001530053	113116718	113117607
ENSE00001530055	113118068	113118161
ENSE00001530056	113118528	113118554

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 98.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7822 / max 155.1186, expressed in 1775 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85783	9.5430	1762
85784	2.0489	1198
85785	0.1903	61

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	98.02	gold quality
cardiac muscle of right atrium	UBERON:0003379	98.00	gold quality
germinal epithelium of ovary	UBERON:0001304	97.76	gold quality
myocardium	UBERON:0002349	97.68	gold quality
heart right ventricle	UBERON:0002080	97.26	gold quality
islet of Langerhans	UBERON:0000006	97.02	gold quality
vastus lateralis	UBERON:0001379	96.98	gold quality
adrenal tissue	UBERON:0018303	96.85	gold quality
epithelial cell of pancreas	CL:0000083	96.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.61	gold quality
quadriceps femoris	UBERON:0001377	96.44	gold quality
heart left ventricle	UBERON:0002084	96.41	gold quality
cardiac ventricle	UBERON:0002082	96.36	gold quality
right atrium auricular region	UBERON:0006631	96.29	gold quality
cardiac atrium	UBERON:0002081	96.24	gold quality
biceps brachii	UBERON:0001507	96.02	gold quality
heart	UBERON:0000948	95.94	gold quality
apex of heart	UBERON:0002098	95.82	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.70	gold quality
amniotic fluid	UBERON:0000173	95.35	gold quality
muscle of leg	UBERON:0001383	95.28	gold quality
gastrocnemius	UBERON:0001388	95.18	gold quality
palpebral conjunctiva	UBERON:0001812	95.03	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.83	gold quality
muscle tissue	UBERON:0002385	94.66	gold quality
skeletal muscle tissue	UBERON:0001134	94.65	gold quality
right adrenal gland cortex	UBERON:0035827	94.57	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.56	gold quality
superficial temporal artery	UBERON:0001614	94.52	gold quality
right adrenal gland	UBERON:0001233	94.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-93593	yes	13.34
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Peptide SMIM30 promotes HCC development by inducing SRC/YES1 membrane anchoring and MAPK pathway activation. (PMID:32461121)
• LINC00998-encoded micropeptide SMIM30 promotes the G1/S transition of cell cycle by regulating cytosolic calcium level. (PMID:36495128)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim30	ENSMUSG00000052419
rattus_norvegicus		ENSRNOG00000088859
rattus_norvegicus		ENSRNOG00000089776

Protein

Protein identifiers

Small integral membrane protein 30 — A4D0T7 (reviewed: A4D0T7)

Alternative names: Microprotein in antiviral immunity 1

All UniProt accessions (1): A4D0T7

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates antiviral innate immune responses. Disrupts the interaction of antiviral protein MAVS with innate immune receptor RIGI and inhibits MAVS aggregation, resulting in the repression of type I interferon signaling and innate immune responses.

Subunit / interactions. Interacts (via transmembrane domain) with antiviral protein MAVS (via transmembrane domain); the interaction disrupts MAVS interaction with RIGI and inhibits MAVS aggregation, resulting in the repression of type I interferon signaling and innate immune responses.

Subcellular location. Endoplasmic reticulum membrane. Mitochondrion membrane.

Induction. Down-regulated following vesicular stomatitis virus (VSV) infection which releases SMIM30-mediated inhibition of the interaction between RIGI and MAVS and leads to the activation of type I interferon signaling and innate immune responses.

RefSeq proteins (2): NP_001339616, NP_001339617* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031742	DUF4730	Family

Pfam: PF15873

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-A4D0T7-F1	85.23	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GOBP_RESPONSE_TO_PEPTIDE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_RESPONSE_TO_TYPE_I_INTERFERON, GOBP_NEGATIVE_REGULATION_OF_INNATE_IMMUNE_RESPONSE, GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_NEGATIVE_REGULATION_OF_DEFENSE_RESPONSE, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_CYTOKINE_STIMULUS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_TYPE_I_INTERFERON_MEDIATED_SIGNALING_PATHWAY

GO Biological Process (3): innate immune response (GO:0045087), negative regulation of type I interferon-mediated signaling pathway (GO:0060339), immune system process (GO:0002376)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): endoplasmic reticulum membrane (GO:0005789), mitochondrial membrane (GO:0031966), mitochondrion (GO:0005739), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle membrane	2
cytoplasm	2
intracellular membrane-bounded organelle	2
immune response	1
defense response to symbiont	1
negative regulation of cytokine-mediated signaling pathway	1
negative regulation of innate immune response	1
type I interferon-mediated signaling pathway	1
regulation of type I interferon-mediated signaling pathway	1
biological_process	1
binding	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
mitochondrion	1
mitochondrial envelope	1
endomembrane system	1
cellular anatomical structure	1

Protein interactions and networks

STRING

116 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM30	SMIM22	K7EJ46	540
SMIM30	NBDY	A0A0U1RRE5	528
SMIM30	YES1	P07947	446
SMIM30	STRIT1	P0DN84	419
SMIM30	UBAP1	Q9NZ09	397
SMIM30	SPATA2L	Q8IUW3	350
SMIM30	NCBP2AS2	Q69YL0	348
SMIM30	GPR85	P60893	337
SMIM30	FHOD3	Q2V2M9	310
SMIM30	MTLN	Q8NCU8	305
SMIM30	FAM120A	Q9NZB2	293
SMIM30	RPS6	P08227	270
SMIM30	KIF5A	Q12840	265
SMIM30	PTGR2	Q8N8N7	258
SMIM30	MRLN	P0DMT0	258

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

Diamond homologs: A4D0T7, F2Z3Y9

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

0 predictions. Top by Δscore:

AlphaMissense

357 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:113117459:G:C	S40R	0.958
7:113117459:G:T	S40R	0.958
7:113117461:T:G	S40R	0.958
7:113117452:C:G	G43R	0.904
7:113117473:C:G	G36R	0.883
7:113117463:A:T	L39H	0.871
7:113117440:A:G	C47R	0.858
7:113117442:G:T	A46D	0.854
7:113117481:A:T	L33H	0.800
7:113117425:C:G	A52P	0.796
7:113117446:A:G	C45R	0.795
7:113117463:A:C	L39R	0.787
7:113117494:C:G	D29H	0.771
7:113117424:G:T	A52E	0.763
7:113117454:G:T	T42K	0.761
7:113117436:A:G	L48S	0.759
7:113117491:C:G	A30P	0.756
7:113117451:C:T	G43D	0.755
7:113117484:G:T	A32D	0.742
7:113117481:A:G	L33P	0.738
7:113117434:C:G	G49R	0.734
7:113117434:C:T	G49R	0.734
7:113117434:C:A	G49W	0.733
7:113117481:A:C	L33R	0.727
7:113117466:A:T	V38D	0.723
7:113117443:C:G	A46P	0.721
7:113117457:A:T	I41N	0.720
7:113117472:C:T	G36D	0.719
7:113117414:T:A	R55S	0.714
7:113117414:T:G	R55S	0.714

dbSNP variants (sampled 300 via entrez): RS1000382504 (7:113118635 C>A,G,T), RS1000988000 (7:113120332 G>A), RS1001813687 (7:113118914 C>T), RS1002656718 (7:113120350 GATA>G), RS1003035268 (7:113120043 A>G,T), RS1003842042 (7:113118078 G>A), RS1004065365 (7:113118810 G>T), RS1004353897 (7:113116507 G>A), RS1004362677 (7:113117638 C>G,T), RS1004548523 (7:113118300 T>C,G), RS1004961276 (7:113119001 G>A), RS1005803462 (7:113119940 T>A), RS1006421671 (7:113120293 A>T), RS1007706784 (7:113119506 C>A), RS1008447307 (7:113116642 T>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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
chloropicrin	decreases expression, affects expression	2
Valproic Acid	decreases methylation, increases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
fipronil	affects cotreatment, increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
ICG 001	decreases expression	1
Temozolomide	decreases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	decreases expression	1
DEET	increases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Smoke	decreases expression, increases abundance	1
Testosterone	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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