STOML1

Summary

STOML1 (stomatin like 1, HGNC:14560) is a protein-coding gene on chromosome 15q24.1, encoding Stomatin-like protein 1 (Q9UBI4). May play a role in cholesterol transfer to late endosomes.

Predicted to enable ion channel inhibitor activity. Predicted to be involved in lipid transport. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in intracellular membrane-bounded organelle.

Source: NCBI Gene 9399 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_004809

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14560
Approved symbol	STOML1
Name	stomatin like 1
Location	15q24.1
Locus type	gene with protein product
Status	Approved
Aliases	hUNC-24, SLP-1, STORP, FLJ36370
Ensembl gene	ENSG00000067221
Ensembl biotype	protein_coding
OMIM	608326
Entrez	9399

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 17 protein_coding, 4 retained_intron

ENST00000316900, ENST00000316911, ENST00000359750, ENST00000541638, ENST00000561480, ENST00000561656, ENST00000562453, ENST00000563229, ENST00000564777, ENST00000565240, ENST00000566081, ENST00000567052, ENST00000567876, ENST00000903410, ENST00000903411, ENST00000903412, ENST00000903413, ENST00000958641, ENST00000958642, ENST00000958643, ENST00000958644

RefSeq mRNA: 12 — MANE Select: NM_004809 NM_001256672, NM_001256673, NM_001256674, NM_001256675, NM_001256676, NM_001256677, NM_001324226, NM_001324227, NM_001324228, NM_001324229, NM_001324230, NM_004809

CCDS: CCDS10254, CCDS58381, CCDS58382, CCDS58383, CCDS58384, CCDS58385

Canonical transcript exons

ENST00000541638 — 7 exons

Exon	Start	End
ENSE00001275911	73985318	73985513
ENSE00001275946	73988599	73988802
ENSE00001276002	73984659	73984871
ENSE00002309628	73978926	73984130
ENSE00003519511	73989108	73989257
ENSE00003671799	73990351	73990457
ENSE00003849711	73992091	73992295

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 95.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0747 / max 125.6237, expressed in 1668 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150876	3.2703	1353
150877	1.8045	1142

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	95.62	gold quality
endothelial cell	CL:0000115	95.45	gold quality
tendon of biceps brachii	UBERON:0008188	94.73	gold quality
frontal pole	UBERON:0002795	94.51	gold quality
prefrontal cortex	UBERON:0000451	94.46	gold quality
superior vestibular nucleus	UBERON:0007227	93.39	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.77	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.60	gold quality
frontal cortex	UBERON:0001870	92.58	gold quality
right frontal lobe	UBERON:0002810	92.18	gold quality
neocortex	UBERON:0001950	92.11	gold quality
cingulate cortex	UBERON:0003027	91.91	gold quality
Brodmann (1909) area 10	UBERON:0013541	91.91	gold quality
anterior cingulate cortex	UBERON:0009835	91.89	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.86	gold quality
cervix squamous epithelium	UBERON:0006922	91.75	gold quality
apex of heart	UBERON:0002098	91.67	gold quality
cerebral cortex	UBERON:0000956	91.28	gold quality
pons	UBERON:0000988	91.00	gold quality
middle temporal gyrus	UBERON:0002771	90.85	gold quality
medulla oblongata	UBERON:0001896	90.72	gold quality
nucleus accumbens	UBERON:0001882	90.62	gold quality
telencephalon	UBERON:0001893	90.51	gold quality
temporal lobe	UBERON:0001871	90.36	gold quality
amygdala	UBERON:0001876	90.35	gold quality
forebrain	UBERON:0001890	89.98	gold quality
entorhinal cortex	UBERON:0002728	89.98	gold quality
superior frontal gyrus	UBERON:0002661	89.89	gold quality
primary visual cortex	UBERON:0002436	89.84	gold quality
dorsal root ganglion	UBERON:0000044	89.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting STOML1, 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-5193	100.00	67.26	1744
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-198	98.70	67.32	920
HSA-MIR-10400-3P	97.29	64.66	597
HSA-MIR-4674	97.29	64.62	597
HSA-MIR-5702	96.68	68.21	958
HSA-MIR-2861	95.24	65.47	1056

Literature-anchored findings (GeneRIF, showing 2)

• Stomatin-like protein-1 interacts with stomatin and is targeted to late endosomes (PMID:19696025)
• [review] Stomatin family member STOML1 is oligomeric; it mostly localizes to membrane domains and has been shown to modulate ion channel activity. (PMID:21501885)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	stoml1	ENSDARG00000062142
mus_musculus	Stoml1	ENSMUSG00000032333
rattus_norvegicus	Stoml1	ENSRNOG00000008530
caenorhabditis_elegans		WBGENE00006761

Paralogs (4): NPHS2 (ENSG00000116218), STOML3 (ENSG00000133115), STOM (ENSG00000148175), STOML2 (ENSG00000165283)

Protein

Protein identifiers

Stomatin-like protein 1 — Q9UBI4 (reviewed: Q9UBI4)

Alternative names: EPB72-like protein 1, Protein unc-24 homolog, Stomatin-related protein

All UniProt accessions (5): Q9UBI4, H3BPC1, H3BQA9, H3BST3, H3BVF2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cholesterol transfer to late endosomes. May play a role in modulating membrane acid-sensing ion channels. Can specifically inhibit proton-gated current of ASIC1 isoform 1. Can increase inactivation speed of ASIC3. May be involved in regulation of proton sensing in dorsal root ganglions. May play a role in protecting FBXW7 isoform 3 from degradation.

Subunit / interactions. Interacts with STOM; may redistribute STOM from the plasma membrane to late endosomes. Interacts with FBXW7 isoform 3 and CDK2.

Subcellular location. Membrane. Late endosome membrane. Membrane raft. Cell membrane. Cytoplasmic vesicle.

Tissue specificity. Ubiquitously expressed at low levels. Expression is highest in brain.

Similarity. Belongs to the band 7/mec-2 family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q9UBI4-1	1	yes
Q9UBI4-2	2
Q9UBI4-3	3
Q9UBI4-4	4
Q9UBI4-5	5
Q9UBI4-6	6

RefSeq proteins (12): NP_001243601, NP_001243602, NP_001243603, NP_001243604, NP_001243605, NP_001243606, NP_001311155, NP_001311156, NP_001311157, NP_001311158, NP_001311159, NP_004800* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001107	Band_7	Domain
IPR001972	Stomatin_HflK_fam	Family
IPR003033	SCP2_sterol-bd_dom	Domain
IPR036013	Band_7/SPFH_dom_sf	Homologous_superfamily
IPR036527	SCP2_sterol-bd_dom_sf	Homologous_superfamily
IPR043202	Band-7_stomatin-like	Family

Pfam: PF01145, PF02036

UniProt features (16 total): sequence conflict 4, splice variant 4, mutagenesis site 2, chain 1, transmembrane region 1, topological domain 1, domain 1, short sequence motif 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UBI4-F1	75.78	0.40

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): 28

Mutagenesis-validated functional residues (2):

Position	Phenotype
7	plasma membrane localization.
10	plasma membrane localization.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, MODULE_66, MODULE_88, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MODULE_11, GOBP_LIPID_LOCALIZATION, MODULE_60, DURCHDEWALD_SKIN_CARCINOGENESIS_UP, RIZKI_TUMOR_INVASIVENESS_3D_UP, GOCC_LATE_ENDOSOME_MEMBRANE, GRYDER_PAX3FOXO1_TOP_ENHANCERS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (1): lipid transport (GO:0006869)

GO Molecular Function (2): ion channel inhibitor activity (GO:0008200), protein binding (GO:0005515)

GO Cellular Component (6): plasma membrane (GO:0005886), late endosome membrane (GO:0031902), membrane raft (GO:0045121), endosome (GO:0005768), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
lipid localization	1
monoatomic ion channel activity	1
channel inhibitor activity	1
transmembrane transporter binding	1
ion channel regulator activity	1
binding	1
membrane	1
cell periphery	1
late endosome	1
endosome membrane	1
membrane microdomain	1
endomembrane system	1
cytoplasmic vesicle	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

3412 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STOML1	UNC119	Q13432	654
STOML1	SDR39U1	Q9NRG7	574
STOML1	EMC1	Q8N766	541
STOML1	NYNRIN	Q9P2P1	540
STOML1	SCP2D1	Q9UJQ7	524
STOML1	CBLN3	Q6UW01	514
STOML1	PHB1	P35232	503
STOML1	SCP2	P22307	484
STOML1	ASIC2	Q16515	483
STOML1	UNC79	Q9P2D8	476
STOML1	UNC13B	O14795	468
STOML1	ASIC3	Q9UHC3	454
STOML1	AJM1	C9J069	452
STOML1	AACS	Q86V21	451
STOML1	LRRC75B	Q2VPJ9	448

IntAct

14 interactions, top by confidence:

A	B	Type	Score
STOML1	STOM	psi-mi:“MI:0403”(colocalization)	0.600
STOM	STOML1	psi-mi:“MI:0915”(physical association)	0.600
STOML1	STOM	psi-mi:“MI:0915”(physical association)	0.600
STOML1	FBXW7	psi-mi:“MI:0915”(physical association)	0.510
FBXW7	STOML1	psi-mi:“MI:0915”(physical association)	0.510
CDK2	STOML1	psi-mi:“MI:0915”(physical association)	0.400
STOML1	CDK2	psi-mi:“MI:0915”(physical association)	0.400
SLC18A2	UBXN8	psi-mi:“MI:0914”(association)	0.350
SLAMF1	ZNF292	psi-mi:“MI:0914”(association)	0.350
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270
STOML1	E2F1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): STOML1 (Affinity Capture-MS), STOML1 (Affinity Capture-MS), STOML1 (Proximity Label-MS), STOML1 (Affinity Capture-MS), STOML1 (Affinity Capture-MS), STOML1 (Affinity Capture-MS), STOML1 (Proximity Label-MS), STOML1 (Proximity Label-MS), STOML1 (Co-fractionation), STOML1 (Co-fractionation), STOML1 (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex), STOML1 (Affinity Capture-Western), FBXW7 (Affinity Capture-Western), CDK2 (Affinity Capture-Western)

ESM2 similar proteins: A1A4J8, A5PK26, O35231, O88396, P19686, P19687, P36407, P48760, P97576, Q07617, Q0P5N5, Q15027, Q1JQC5, Q1L5Z9, Q32KL4, Q3SZC1, Q3UY23, Q4G069, Q4R380, Q502I6, Q5R435, Q5R8E4, Q5RA81, Q5U2X2, Q60443, Q6DKK2, Q6PBQ2, Q7SXA9, Q80VP5, Q80Y81, Q80ZX8, Q8BMS4, Q8BUI3, Q8C9A2, Q8CGS5, Q8CI66, Q8IWL3, Q8K2H4, Q8K3A0, Q8NFF5

Diamond homologs: A0A097ZPE8, A0A144Y7G4, A0A162J3X8, A0A1L5BU05, A0A1V0QSC6, A0A2H3D8Y2, A0R518, A3LZU7, A4FUZ6, A6SSW9, C1DMX5, D4Z260, F1QWW8, M2ZIX7, O75911, O77769, O86034, O88876, P07857, P0A2D1, P0A2D2, P0AET8, P0AET9, P0CU75, P0DX40, P0DXE0, P11915, P12310, P14802, P21215, P22307, P22414, P22441, P25145, P28643, P33207, P37440, P37694, P40747, P46331

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1130 predictions. Top by Δscore:

Variant	Effect	Δscore
15:73984127:CGTC:C	acceptor_gain	1.0000
15:73984128:GTC:G	acceptor_gain	1.0000
15:73984129:TC:T	acceptor_gain	1.0000
15:73984130:CC:C	acceptor_gain	1.0000
15:73984130:CCT:C	acceptor_loss	1.0000
15:73984131:C:CC	acceptor_gain	1.0000
15:73984132:T:C	acceptor_loss	1.0000
15:73984139:C:CT	acceptor_gain	1.0000
15:73985315:CACC:C	donor_loss	1.0000
15:73985316:A:C	donor_loss	1.0000
15:73985317:C:CA	donor_loss	1.0000
15:73985340:T:TA	donor_gain	1.0000
15:73985361:T:TA	donor_gain	1.0000
15:73985509:TCCAG:T	acceptor_gain	1.0000
15:73985510:CCAG:C	acceptor_gain	1.0000
15:73985510:CCAGC:C	acceptor_gain	1.0000
15:73985511:CAG:C	acceptor_gain	1.0000
15:73985511:CAGC:C	acceptor_gain	1.0000
15:73985512:AG:A	acceptor_gain	1.0000
15:73985512:AGCTG:A	acceptor_loss	1.0000
15:73985514:C:CC	acceptor_gain	1.0000
15:73985522:CAG:C	acceptor_gain	1.0000
15:73985523:A:T	acceptor_gain	1.0000
15:73985524:G:C	acceptor_gain	1.0000
15:73985524:G:GC	acceptor_gain	1.0000
15:73988593:GCCTA:G	donor_loss	1.0000
15:73988594:CCTA:C	donor_loss	1.0000
15:73988595:CTAC:C	donor_loss	1.0000
15:73988596:TA:T	donor_loss	1.0000
15:73988597:A:AC	donor_gain	1.0000

AlphaMissense

2554 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:73985482:C:T	G209E	0.999
15:73985483:C:G	G209R	0.999
15:73985483:C:T	G209R	0.999
15:73988759:A:T	V145D	0.999
15:73985479:A:G	L210P	0.998
15:73985483:C:A	G209W	0.998
15:73988684:G:T	A170D	0.998
15:73985486:A:G	W208R	0.997
15:73985486:A:T	W208R	0.997
15:73988685:C:G	A170P	0.997
15:73988750:C:G	R148P	0.997
15:73989121:A:T	V126D	0.997
15:73985482:C:A	G209V	0.996
15:73988752:A:C	F147L	0.996
15:73988752:A:T	F147L	0.996
15:73988754:A:G	F147L	0.996
15:73989238:C:G	R87P	0.996
15:73989126:G:C	F124L	0.995
15:73989126:G:T	F124L	0.995
15:73989128:A:G	F124L	0.995
15:73989139:C:A	R120M	0.995
15:73988753:A:G	F147S	0.994
15:73988766:C:G	A143P	0.994
15:73989138:C:A	R120S	0.994
15:73989138:C:G	R120S	0.994
15:73989139:C:G	R120T	0.994
15:73989163:T:A	D112V	0.994
15:73985473:A:T	V212E	0.993
15:73988603:A:G	L197P	0.993
15:73988693:C:G	R167P	0.993

dbSNP variants (sampled 300 via entrez): RS1000053277 (15:73981625 G>C), RS1000105189 (15:73981316 G>A), RS1000490083 (15:73983130 A>G), RS1000500043 (15:73995711 T>A), RS1000604037 (15:73988113 G>C), RS1000676246 (15:73988417 C>A), RS1000784898 (15:73981924 A>T), RS1000841062 (15:73983407 C>G), RS1000954489 (15:73995261 T>C,G), RS1000956473 (15:73995305 TA>T), RS1001161123 (15:73994925 G>A,C), RS1001304039 (15:73986300 C>T), RS1001337942 (15:73987874 C>T), RS1001572485 (15:73981022 G>A), RS1001839518 (15:73987601 G>A)

Disease associations

OMIM: gene MIM:608326 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005196_10	Coronary artery disease	7.000000e-07
GCST012227_300	Hip circumference adjusted for BMI	2.000000e-13
GCST90020028_1745	Hip circumference adjusted for BMI	1.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	4
Valproic Acid	affects expression, increases expression, increases methylation	3
Tobacco Smoke Pollution	decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
benzo(e)pyrene	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Calcitriol	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	increases expression	1
Formaldehyde	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
Vitamin E	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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