SMIM10L1

Summary

SMIM10L1 (small integral membrane protein 10 like 1, HGNC:49847) is a protein-coding gene on chromosome 12p13.2, encoding Small integral membrane protein 10-like protein 1 (P0DMW3).

Located in mitochondrion.

Source: NCBI Gene 100129361 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001271592

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49847
Approved symbol	SMIM10L1
Name	small integral membrane protein 10 like 1
Location	12p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000256537
Ensembl biotype	protein_coding
Entrez	100129361

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000622602

RefSeq mRNA: 1 — MANE Select: NM_001271592 NM_001271592

CCDS: CCDS81667

Canonical transcript exons

ENST00000622602 — 1 exons

Exon	Start	End
ENSE00003738263	11171194	11176016

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 87.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.0579 / max 341.8678, expressed in 1821 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
124199	55.7310	1821
124200	1.3269	698

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	87.86	gold quality
muscle of leg	UBERON:0001383	87.26	gold quality
right adrenal gland cortex	UBERON:0035827	86.74	gold quality
right adrenal gland	UBERON:0001233	86.31	gold quality
left adrenal gland	UBERON:0001234	86.03	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.93	gold quality
substantia nigra	UBERON:0002038	85.91	gold quality
left adrenal gland cortex	UBERON:0035825	85.17	gold quality
heart left ventricle	UBERON:0002084	85.00	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.84	gold quality
Ammon’s horn	UBERON:0001954	84.81	gold quality
adrenal gland	UBERON:0002369	84.77	gold quality
putamen	UBERON:0001874	84.56	gold quality
amygdala	UBERON:0001876	84.43	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.39	gold quality
temporal lobe	UBERON:0001871	84.33	gold quality
hypothalamus	UBERON:0001898	84.29	gold quality
heart	UBERON:0000948	83.89	gold quality
nucleus accumbens	UBERON:0001882	83.74	gold quality
skeletal muscle tissue	UBERON:0001134	83.64	gold quality
right atrium auricular region	UBERON:0006631	83.06	gold quality
anterior cingulate cortex	UBERON:0009835	83.04	gold quality
superior frontal gyrus	UBERON:0002661	83.00	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.98	gold quality
cerebral cortex	UBERON:0000956	82.92	gold quality
caudate nucleus	UBERON:0001873	82.65	gold quality
prefrontal cortex	UBERON:0000451	82.64	gold quality
muscle tissue	UBERON:0002385	82.45	gold quality
frontal cortex	UBERON:0001870	82.37	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-112	yes	6.49
E-ANND-3	no	1.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

133 targeting SMIM10L1, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
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-3148	99.97	75.06	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-9902	99.89	69.15	2250

Literature-anchored findings (GeneRIF, showing 1)

• Small integral membrane protein 10 like 1 downregulation enhances differentiation of adipose progenitor cells. (PMID:35290761)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim10l3	ENSDARG00000100331
mus_musculus	Smim10l1	ENSMUSG00000072704
rattus_norvegicus	Smim10l1	ENSRNOG00000047309

Paralogs (4): SMIM10L2A (ENSG00000178947), SMIM10 (ENSG00000184785), SMIM10L2B (ENSG00000196972), SMIM10L3 (ENSG00000286075)

Protein

Protein identifiers

Small integral membrane protein 10-like protein 1 — P0DMW3 (reviewed: P0DMW3)

All UniProt accessions (1): P0DMW3

RefSeq proteins (1): NP_001258521* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029367	SMIM10	Family

Pfam: PF15118

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DMW3-F1	69.27	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, CADWELL_ATG16L1_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, MULLIGHAN_MLL_SIGNATURE_1_UP, TIEN_INTESTINE_PROBIOTICS_6HR_DN, SNF5_DN.V1_DN, ATF5_TARGET_GENES, NKX2_2_TARGET_GENES, SETD7_TARGET_GENES, ZNF22_TARGET_GENES, ZNF30_TARGET_GENES, ZNF33A_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

36 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM10L1	TNS2	Q63HR2	433
SMIM10L1	TNS4	Q8IZW8	432
SMIM10L1	TNS3	Q68CZ2	399
SMIM10L1	TNS1	Q9HBL0	396
SMIM10L1	SREBF1	P36956	192
SMIM10L1	TRIT1	Q9H3H1	166
SMIM10L1	DNPEP	Q9ULA0	161
SMIM10L1	IWS1	Q96ST2	158
SMIM10L1	TMEM254	Q8TBM7	154
SMIM10L1	WDR31	Q8NA23	143
SMIM10L1	RACK1	P25388	143
SMIM10L1	PTEN	P60484	120
SMIM10L1	DCAF7	P61962	91
SMIM10L1	UTP20	O75691	0
SMIM10L1	TOMM6	Q96B49	0
SMIM10L1	MUC15	Q8N387	0
SMIM10L1	AOAH	P28039	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0D1DMK2, A0A1B0GUV1, A8MUN3, A9G6D9, B8DP12, L7N648, O90299, P03294, P06791, P0C5K6, P0C854, P0DMW3, P15099, P16791, P16835, P25620, P34245, P40057, P53211, P69616, P69617, P75410, Q04612, Q07649, Q08419, Q32L37, Q3BSH4, Q494R0, Q53513, Q5YCU7, Q5YCU8, Q64747, Q64902, Q6J1A5, Q6J8G1, Q6Q572, Q6REU5, Q6UXP9, Q6ZS49, Q6ZUT4

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

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

151 predictions. Top by Δscore:

Variant	Effect	Δscore
12:11171265:ACCGT:A	donor_gain	0.9800
12:11171266:CCGTC:C	donor_gain	0.9800
12:11171547:TGCAG:T	donor_loss	0.9700
12:11171549:CAGGT:C	donor_loss	0.9700
12:11171550:AG:A	donor_loss	0.9700
12:11171551:GG:G	donor_loss	0.9700
12:11171552:G:GC	donor_loss	0.9700
12:11171553:T:G	donor_loss	0.9700
12:11171261:GCTT:G	donor_loss	0.9400
12:11171262:CTTA:C	donor_loss	0.9400
12:11171263:TTA:T	donor_loss	0.9400
12:11171264:TACC:T	donor_loss	0.9400
12:11171265:ACC:A	donor_loss	0.9400
12:11171266:C:CG	donor_loss	0.9400
12:11171269:T:TA	donor_gain	0.9100
12:11171265:A:AC	donor_gain	0.9000
12:11171266:C:CC	donor_gain	0.9000
12:11171266:CCGT:C	donor_gain	0.8900
12:11171531:A:AG	donor_gain	0.8200
12:11175885:TAAG:T	acceptor_gain	0.8200
12:11171259:TTGC:T	donor_loss	0.7900
12:11171260:TGCT:T	donor_loss	0.7900
12:11171465:G:A	donor_gain	0.7800
12:11172242:A:AG	donor_gain	0.7800
12:11172243:G:GG	donor_gain	0.7800
12:11172247:A:G	donor_gain	0.7800
12:11175886:AAGG:A	acceptor_gain	0.7600
12:11171258:TTTGC:T	donor_loss	0.7500
12:11171413:GACAC:G	donor_loss	0.7300
12:11171414:ACAC:A	donor_loss	0.7300

AlphaMissense

424 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:11171435:T:C	F27L	0.985
12:11171437:C:A	F27L	0.985
12:11171437:C:G	F27L	0.985
12:11171522:G:C	G56R	0.985
12:11171471:T:C	F39L	0.984
12:11171473:C:A	F39L	0.984
12:11171473:C:G	F39L	0.984
12:11171523:G:A	G56D	0.983
12:11171547:T:C	L64S	0.980
12:11171481:C:A	A42D	0.977
12:11171501:T:C	F49L	0.977
12:11171503:C:A	F49L	0.977
12:11171503:C:G	F49L	0.977
12:11171448:T:A	L31H	0.975
12:11171471:T:A	F39I	0.975
12:11171502:T:C	F49S	0.975
12:11171520:C:A	A55E	0.974
12:11171502:T:G	F49C	0.973
12:11171517:T:A	V54D	0.972
12:11171451:C:T	S32F	0.971
12:11171525:T:C	S57P	0.969
12:11171529:T:A	V58E	0.965
12:11171460:T:C	L35P	0.962
12:11171485:G:C	W43C	0.962
12:11171485:G:T	W43C	0.962
12:11171490:T:C	L45P	0.961
12:11171513:T:G	Y53D	0.961
12:11171478:T:C	L41P	0.959
12:11171436:T:C	F27S	0.958
12:11171451:C:A	S32Y	0.958

dbSNP variants (sampled 300 via entrez): RS1000099420 (12:11173496 G>T), RS1000422884 (12:11170853 A>G), RS1000874378 (12:11169820 G>A), RS1001132920 (12:11174181 GACAAA>G), RS1001867940 (12:11175294 A>G), RS1002079424 (12:11170156 G>A,T), RS1002088914 (12:11173330 C>CA), RS1002299298 (12:11175509 G>A,C), RS1002538872 (12:11172507 A>G,T), RS1002981587 (12:11172801 C>T), RS1003220351 (12:11171010 T>C), RS1003947269 (12:11173896 C>T), RS1004244144 (12:11171516 G>A,C), RS1004306341 (12:11176465 G>A), RS1004617297 (12:11171289 G>A,C,T)

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

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects methylation	1
sodium arsenite	increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Gold Compounds	decreases expression	1

Clinical trials (associated diseases)

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