SMIM10

Summary

SMIM10 (small integral membrane protein 10, HGNC:41913) is a protein-coding gene on chromosome Xq26.3, encoding Small integral membrane protein 10 (Q96HG1).

Predicted to be located in membrane.

Source: NCBI Gene 644538 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001163438

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41913
Approved symbol	SMIM10
Name	small integral membrane protein 10
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184785
Ensembl biotype	protein_coding
Entrez	644538

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000330288

RefSeq mRNA: 1 — MANE Select: NM_001163438 NM_001163438

CCDS: CCDS55502

Canonical transcript exons

ENST00000330288 — 1 exons

Exon	Start	End
ENSE00001324955	134990991	134992473

Expression profiles

Bgee: expression breadth ubiquitous, 176 present calls, max score 94.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4502 / max 99.4042, expressed in 1271 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197619	7.1419	1268
197617	0.1753	93
197618	0.1331	57

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
popliteal artery	UBERON:0002250	94.20	gold quality
tibial artery	UBERON:0007610	94.19	gold quality
right coronary artery	UBERON:0001625	94.13	gold quality
calcaneal tendon	UBERON:0003701	92.98	gold quality
left coronary artery	UBERON:0001626	92.89	gold quality
aorta	UBERON:0000947	92.64	gold quality
coronary artery	UBERON:0001621	91.73	gold quality
thoracic aorta	UBERON:0001515	90.99	gold quality
ascending aorta	UBERON:0001496	90.90	gold quality
descending thoracic aorta	UBERON:0002345	90.79	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.55	gold quality
right testis	UBERON:0004534	89.16	gold quality
left testis	UBERON:0004533	88.20	gold quality
buccal mucosa cell	CL:0002336	88.07	silver quality
spinal cord	UBERON:0002240	87.76	gold quality
tibial nerve	UBERON:0001323	87.21	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.77	gold quality
lower esophagus	UBERON:0013473	86.71	gold quality
testis	UBERON:0000473	86.52	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	86.36	gold quality
left uterine tube	UBERON:0001303	86.10	gold quality
left adrenal gland cortex	UBERON:0035825	85.90	gold quality
left adrenal gland	UBERON:0001234	85.75	gold quality
endocervix	UBERON:0000458	85.26	gold quality
right adrenal gland	UBERON:0001233	85.14	gold quality
mucosa of stomach	UBERON:0001199	84.67	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.67	gold quality
right adrenal gland cortex	UBERON:0035827	84.41	gold quality
body of uterus	UBERON:0009853	84.25	gold quality
adrenal cortex	UBERON:0001235	84.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-6	yes	52.82
E-ANND-3	yes	5.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting SMIM10, 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-3064-3P	100.00	70.09	1254
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-6758-3P	99.57	67.55	1078
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-6734-3P	99.15	66.27	1627

Literature-anchored findings (GeneRIF, showing 1)

• Therefore, these data suggest that SMIM10 exerts an oncosuppressive role in melanoma cells.Taken together, our results unveil the potential of S. cerevisiae to study hBRAFV600E, to populate the network of its functional interactors and, in doing so, to uncover new cancer-associated genes with therapeutic potential (PMID:30237439)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim10l3	ENSDARG00000100331

Paralogs (4): SMIM10L2A (ENSG00000178947), SMIM10L2B (ENSG00000196972), SMIM10L1 (ENSG00000256537), SMIM10L3 (ENSG00000286075)

Protein

Protein identifiers

Small integral membrane protein 10 — Q96HG1 (reviewed: Q96HG1)

All UniProt accessions (1): Q96HG1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001156910* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029367	SMIM10	Family

Pfam: PF15118

UniProt features (2 total): chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HG1-F1	67.05	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, chrXq26, RYBP_TARGET_GENES, ZNF2_TARGET_GENES, ZNF592_TARGET_GENES, ZNF618_TARGET_GENES, ZNF660_TARGET_GENES, ZSCAN30_TARGET_GENES, MIR7856_5P, MIR3978, MIR4743_3P, MIR4297, MIR3977, MIR4330, GSE12366_NAIVE_VS_MEMORY_BCELL_UP

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

6 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM10	BRAF	P15056	257
SMIM10	MUC15	Q8N387	0
SMIM10	TOMM6	Q96B49	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A023PXF2, A0A0C4DGP1, A0LE50, A6X974, C0QIZ2, I2HB70, O30141, O60756, P05678, P0C5L6, P0DQF8, P0DXX6, P11304, P17142, P34249, P36153, P38470, P38726, P39550, P39566, P40326, P40365, P40521, P40551, P40575, P40895, P47020, P53056, P54949, P59471, P87264, P92534, P93284, P93302, Q02918, Q03913, Q04909, Q12506, Q3E7Z1, Q5QFB9

Diamond homologs: A0A0C4DGP1, P0DMW3, P0DMW4, P0DMW5, Q5U425, Q96HG1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

85 predictions. Top by Δscore:

Variant	Effect	Δscore
X:134991490:A:AG	acceptor_gain	0.5400
X:134991491:G:GG	acceptor_gain	0.5400
X:134991331:TGCAG:T	donor_loss	0.5000
X:134991333:CAG:C	donor_loss	0.5000
X:134991334:AG:A	donor_loss	0.5000
X:134991335:GG:G	donor_loss	0.5000
X:134991336:G:GA	donor_loss	0.5000
X:134991337:T:G	donor_loss	0.5000
X:134991316:T:G	donor_gain	0.4500
X:134991995:C:G	acceptor_gain	0.4500
X:134991028:G:GT	donor_gain	0.4200
X:134991333:C:T	donor_gain	0.3900
X:134991073:GGTCG:G	donor_gain	0.3700
X:134991074:GTCGG:G	donor_gain	0.3700
X:134991075:TCGGT:T	donor_gain	0.3700
X:134991315:A:AG	donor_gain	0.3600
X:134991925:A:C	acceptor_gain	0.3500
X:134991074:GTCG:G	donor_gain	0.3300
X:134991492:T:G	acceptor_gain	0.3300
X:134991994:A:AG	acceptor_gain	0.3300
X:134992032:A:AG	acceptor_gain	0.3300
X:134992033:G:GG	acceptor_gain	0.3300
X:134991491:GTAT:G	acceptor_gain	0.3200
X:134991338:A:G	donor_loss	0.3000
X:134991491:GTATA:G	acceptor_gain	0.2900
X:134991083:TC:T	donor_gain	0.2800
X:134991899:TGG:T	acceptor_gain	0.2800
X:134991921:CCCAA:C	acceptor_gain	0.2800
X:134991491:GT:G	acceptor_gain	0.2700
X:134991076:C:CA	donor_gain	0.2600

AlphaMissense

518 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:134991219:T:C	F42L	0.924
X:134991221:C:A	F42L	0.924
X:134991221:C:G	F42L	0.924
X:134991255:T:C	F54L	0.886
X:134991257:C:A	F54L	0.886
X:134991257:C:G	F54L	0.886
X:134991285:T:C	F64L	0.817
X:134991287:C:A	F64L	0.817
X:134991287:C:G	F64L	0.817
X:134991265:C:A	A57D	0.719
X:134991252:T:C	F53L	0.712
X:134991254:C:A	F53L	0.712
X:134991254:C:G	F53L	0.712
X:134991227:G:C	K44N	0.706
X:134991227:G:T	K44N	0.706
X:134991269:G:C	W58C	0.685
X:134991269:G:T	W58C	0.685
X:134991267:T:A	W58R	0.670
X:134991267:T:C	W58R	0.670
X:134991232:T:A	L46H	0.661
X:134991255:T:A	F54I	0.659
X:134991307:C:A	A71D	0.647
X:134991220:T:G	F42C	0.644
X:134991220:T:C	F42S	0.636
X:134991276:C:A	R61S	0.617
X:134991235:C:A	T47K	0.607
X:134991256:T:G	F54C	0.599
X:134991313:T:A	V73E	0.586

dbSNP variants (sampled 300 via entrez): RS1000713221 (X:134991831 T>C), RS1002215013 (X:134990821 C>T), RS1002568923 (X:134990169 A>G), RS1002928843 (X:134992039 G>A), RS1004186601 (X:134990030 T>C), RS1004217889 (X:134989361 T>G), RS1004238998 (X:134990747 T>A), RS1004551165 (X:134992636 T>G), RS1005678328 (X:134989592 C>T), RS1005921312 (X:134989039 G>C,T), RS1011768781 (X:134992566 G>A), RS1011911147 (X:134989428 C>T), RS1012950181 (X:134992026 T>C), RS1013331536 (X:134991317 T>C), RS1013481295 (X:134991724 A>AG)

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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Diethylstilbestrol	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Nickel	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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