SNN

Summary

SNN (stannin, HGNC:11149) is a protein-coding gene on chromosome 16p13.13, encoding Stannin (O75324). Plays a role in the toxic effects of organotins.

Enables metal ion binding activity. Predicted to be involved in response to toxic substance. Located in cytoplasm and membrane.

Source: NCBI Gene 8303 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_003498

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11149
Approved symbol	SNN
Name	stannin
Location	16p13.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184602
Ensembl biotype	protein_coding
OMIM	603032
Entrez	8303

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000329565, ENST00000907333, ENST00000907334, ENST00000907335, ENST00000907336, ENST00000907337, ENST00000924278, ENST00000924279, ENST00000924280, ENST00000924281, ENST00000924282, ENST00000960815, ENST00000960816, ENST00000960817, ENST00000960818, ENST00000960819

RefSeq mRNA: 1 — MANE Select: NM_003498 NM_003498

CCDS: CCDS10549

Canonical transcript exons

ENST00000329565 — 2 exons

Exon	Start	End
ENSE00001292015	11675975	11679152
ENSE00001489923	11668455	11668540

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 99.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.3550 / max 417.5166, expressed in 1676 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152795	16.3550	1676

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	99.08	gold quality
endothelial cell	CL:0000115	98.99	gold quality
lateral globus pallidus	UBERON:0002476	98.91	gold quality
entorhinal cortex	UBERON:0002728	98.68	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.54	gold quality
CA1 field of hippocampus	UBERON:0003881	98.52	gold quality
putamen	UBERON:0001874	98.50	gold quality
cortical plate	UBERON:0005343	98.46	gold quality
caudate nucleus	UBERON:0001873	98.40	gold quality
superior frontal gyrus	UBERON:0002661	98.23	gold quality
postcentral gyrus	UBERON:0002581	98.20	gold quality
monocyte	CL:0000576	98.19	gold quality
nucleus accumbens	UBERON:0001882	98.15	gold quality
mononuclear cell	CL:0000842	98.10	gold quality
parietal lobe	UBERON:0001872	98.02	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	97.95	gold quality
right frontal lobe	UBERON:0002810	97.94	gold quality
leukocyte	CL:0000738	97.89	gold quality
temporal lobe	UBERON:0001871	97.88	gold quality
Brodmann (1909) area 46	UBERON:0006483	97.85	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.74	gold quality
globus pallidus	UBERON:0001875	97.69	gold quality
orbitofrontal cortex	UBERON:0004167	97.69	gold quality
medial globus pallidus	UBERON:0002477	97.66	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.61	gold quality
Ammon’s horn	UBERON:0001954	97.58	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.54	gold quality
amygdala	UBERON:0001876	97.52	gold quality
telencephalon	UBERON:0001893	97.50	gold quality
ganglionic eminence	UBERON:0004023	97.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.12
E-MTAB-5061	no	3.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

130 targeting SNN, 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-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3617-3P	99.98	67.86	918
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-4650-5P	99.98	64.69	999
HSA-MIR-590-3P	99.96	74.34	6478
HSA-LET-7D-5P	99.96	71.76	1632

Literature-anchored findings (GeneRIF, showing 1)

• The authors show that stannin interacts with human papillomavirus 16 L1 major capsid protein and impairs the interaction of the L2 minor capsid protein with retromer, which is required for virus trafficking to the trans-Golgi network. (PMID:29058661)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	snn	ENSDARG00000099888
mus_musculus	Snn	ENSMUSG00000037972
rattus_norvegicus	Snn	ENSRNOG00000058739
rattus_norvegicus	Snn	ENSRNOG00000068712

Protein

Protein identifiers

Stannin — O75324 (reviewed: O75324)

Alternative names: AG8_1

All UniProt accessions (1): O75324

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the toxic effects of organotins. Plays a role in endosomal maturation.

Subunit / interactions. Monomer.

Subcellular location. Mitochondrion outer membrane.

Similarity. Belongs to the stannin family.

RefSeq proteins (1): NP_003489* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR015135	SNN_transmemb	Domain
IPR015136	SNN_linker	Domain
IPR015137	SNN_cytoplasm	Domain
IPR027435	Stannin_sf	Homologous_superfamily
IPR038747	Stannin	Family

Pfam: PF09049, PF09050, PF09051

UniProt features (14 total): turn 4, topological domain 2, helix 2, sequence variant 2, chain 1, strand 1, transmembrane region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
1ZZA	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75324-F1	65.32	0.20

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 (1): 49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 259 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GSE45365_NK_CELL_VS_CD8A_DC_UP, CHUNG_BLISTER_CYTOTOXICITY_DN, CROONQUIST_NRAS_SIGNALING_UP, CAGCTG_AP4_Q5, MODULE_75, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, FOSTER_TOLERANT_MACROPHAGE_UP, CCTGTGA_MIR513, MODULE_99, GOCC_MITOCHONDRIAL_ENVELOPE, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, AACTTT_UNKNOWN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, GOBP_RESPONSE_TO_TOXIC_SUBSTANCE

GO Biological Process (1): response to toxic substance (GO:0009636)

GO Molecular Function (1): metal ion binding (GO:0046872)

GO Cellular Component (4): cytoplasm (GO:0005737), mitochondrial outer membrane (GO:0005741), membrane (GO:0016020), mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
response to chemical	1
cation binding	1
intracellular anatomical structure	1
mitochondrial membrane	1
organelle outer membrane	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNN	TXNDC11	Q6PKC3	557
SNN	TMEM61	Q8N0U2	370
SNN	RNF207	Q6ZRF8	368
SNN	GPR153	Q6NV75	367
SNN	CIAO3	Q9H6Q4	361
SNN	TMEM207	Q6UWW9	350
SNN	SMIM22	K7EJ46	348
SNN	OBSL1	O75147	331
SNN	THAP12	O43422	328
SNN	MYPOP	Q86VE0	327
SNN	APOL3	O95236	316
SNN	PNMT	P11086	313
SNN	TMEM213	A2RRL7	307
SNN	ARPC4	P59998	305
SNN	SLN	O00631	302

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SNN	MTDH	psi-mi:“MI:0914”(association)	0.530
TMX1	PLXNB2	psi-mi:“MI:0914”(association)	0.530

BioGRID (11): MTDH (Affinity Capture-MS), TMX1 (Affinity Capture-MS), TES (Affinity Capture-MS), C1orf131 (Affinity Capture-MS), SNN (Affinity Capture-RNA), SNN (Affinity Capture-RNA), TMX1 (Affinity Capture-MS), TES (Affinity Capture-MS), MTDH (Affinity Capture-MS), SNN (Affinity Capture-MS), SNN (Affinity Capture-Luminescence)

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSZ0, A0A1B0GVT2, A0A590UK83, A0PK05, A2VDU1, A2VE22, A4QNL6, A5D7B5, A5D992, O43609, O75324, P0DKX4, P29414, P61807, P61808, Q0VFM5, Q15053, Q16655, Q17Q87, Q1L0X2, Q2KIK3, Q2TBG9, Q3MHM8, Q498C7, Q4V921, Q58CU5, Q5RBD8, Q5RF07, Q5RGQ8, Q64448, Q6UWT2, Q80ZU4, Q8BGN6, Q8BUM6, Q8C3K5, Q8C817, Q8K1D8, Q8N6S5, Q91VT8

Diamond homologs: O75324, P61807, P61808, Q17Q87

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

644 predictions. Top by Δscore:

Variant	Effect	Δscore
16:11668538:ATGGT:A	donor_loss	1.0000
16:11668539:TGGT:T	donor_loss	1.0000
16:11668541:GTGA:G	donor_loss	1.0000
16:11668541:G:GG	donor_gain	0.9900
16:11668542:T:G	donor_loss	0.9900
16:11675969:TTTCA:T	acceptor_loss	0.9900
16:11675971:TCAG:T	acceptor_loss	0.9900
16:11675973:A:AG	acceptor_gain	0.9900
16:11675973:A:C	acceptor_loss	0.9900
16:11675973:AG:A	acceptor_gain	0.9900
16:11675974:G:A	acceptor_loss	0.9900
16:11675974:G:GA	acceptor_gain	0.9900
16:11675974:GG:G	acceptor_gain	0.9900
16:11675974:GGA:G	acceptor_gain	0.9900
16:11675974:GGACT:G	acceptor_gain	0.9900
16:11668539:TG:T	donor_gain	0.9800
16:11668540:GG:G	donor_gain	0.9800
16:11675974:GGAC:G	acceptor_gain	0.9600
16:11675965:T:TA	acceptor_gain	0.9500
16:11668538:ATG:A	donor_gain	0.9300
16:11668776:G:GT	donor_gain	0.9200
16:11668856:C:G	donor_gain	0.9100
16:11669397:G:GT	donor_gain	0.9000
16:11675972:CAGGA:C	acceptor_gain	0.8900
16:11668536:CCATG:C	donor_gain	0.8800
16:11668543:GA:G	donor_loss	0.8700
16:11668903:G:GT	donor_gain	0.8500
16:11669385:C:T	donor_gain	0.8400
16:11670708:G:GG	donor_gain	0.8400
16:11675973:AGGAC:A	acceptor_gain	0.7800

AlphaMissense

562 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:11676135:G:A	G26R	0.997
16:11676135:G:C	G26R	0.997
16:11676150:G:C	G31R	0.996
16:11676151:G:A	G31D	0.995
16:11676115:T:A	L19H	0.993
16:11676121:C:A	A21D	0.993
16:11676127:C:A	A23E	0.993
16:11676115:T:G	L19R	0.991
16:11676136:G:A	G26E	0.991
16:11676237:T:C	F60L	0.991
16:11676239:C:A	F60L	0.991
16:11676239:C:G	F60L	0.991
16:11676130:C:A	A24D	0.990
16:11676109:T:A	V17D	0.989
16:11676153:T:C	C32R	0.989
16:11676100:C:A	T14K	0.985
16:11676133:T:G	L25R	0.985
16:11676115:T:C	L19P	0.984
16:11676133:T:C	L25P	0.984
16:11676133:T:A	L25Q	0.983
16:11676103:T:A	V15D	0.982
16:11676118:T:A	I20N	0.982
16:11676100:C:G	T14R	0.981
16:11676120:G:C	A21P	0.980
16:11676238:T:C	F60S	0.980
16:11676139:C:A	A27D	0.979
16:11676204:A:C	S49R	0.979
16:11676206:C:A	S49R	0.979
16:11676206:C:G	S49R	0.979
16:11676129:G:C	A24P	0.976

dbSNP variants (sampled 300 via entrez): RS1000211768 (16:11669608 C>A,T), RS1000531134 (16:11670860 C>A,T), RS1001524302 (16:11672926 G>A), RS1001630298 (16:11677917 C>G,T), RS1001811357 (16:11674126 G>A,T), RS1002098605 (16:11676965 G>A,C), RS1002149796 (16:11672376 C>T), RS1002166525 (16:11675891 G>A), RS1002367926 (16:11678986 CTG>C), RS1002427985 (16:11674323 C>T), RS1002482030 (16:11673592 C>T), RS1002572693 (16:11677035 C>T), RS1002776769 (16:11669024 C>T), RS1002940917 (16:11671731 G>A), RS1002994592 (16:11667296 G>A)

Disease associations

OMIM: gene MIM:603032 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000363_8	QT interval	5.000000e-15
GCST006043_1	Plasma renin activity levels	3.000000e-07
GCST011347_48	Low density lipoprotein cholesterol levels	1.000000e-08
GCST90013406_18	Liver enzyme levels (alkaline phosphatase)	9.000000e-23

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004682	QT interval
EFO:0006828	plasma renin activity measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Leflunomide	decreases expression	2
Benzo(a)pyrene	affects expression, decreases methylation, increases methylation	2
Tretinoin	increases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	increases expression	2
pirinixic acid	affects binding, decreases expression, increases activity	1
trichostatin A	affects expression	1
sodium arsenite	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
nutlin 3	increases expression, affects cotreatment	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, increases methylation	1
jinfukang	increases expression	1
Valsartan	decreases reaction, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Vincristine	increases expression	1

Clinical trials (associated diseases)

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