STOML3

Summary

STOML3 (stomatin like 3, HGNC:19420) is a protein-coding gene on chromosome 13q13.2, encoding Stomatin-like protein 3 (Q8TAV4). Required for the function of many mechanoreceptors.

Predicted to act upstream of or within signal transduction. Predicted to be located in cilium; membrane raft; and neuron projection. Predicted to be active in plasma membrane.

Source: NCBI Gene 161003 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 71 total
• MANE Select transcript: NM_145286

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19420
Approved symbol	STOML3
Name	stomatin like 3
Location	13q13.2
Locus type	gene with protein product
Status	Approved
Aliases	SRO, Epb7.2l
Ensembl gene	ENSG00000133115
Ensembl biotype	protein_coding
OMIM	608327
Entrez	161003

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000379631, ENST00000423210, ENST00000880988

RefSeq mRNA: 2 — MANE Select: NM_145286 NM_001144033, NM_145286

CCDS: CCDS45040, CCDS9367

Canonical transcript exons

ENST00000379631 — 7 exons

Exon	Start	End
ENSE00000907478	38968400	38968534
ENSE00000907479	38970185	38970388
ENSE00000907480	38972512	38972594
ENSE00000907481	38976540	38976612
ENSE00000907482	38976694	38976797
ENSE00001822857	38965925	38967049
ENSE00001882958	38990670	38990831

Expression profiles

Bgee: expression breadth broad, 63 present calls, max score 94.11.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1512 / max 34.4372, expressed in 61 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136869	0.1374	58
136870	0.0137	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.11	gold quality
right uterine tube	UBERON:0001302	93.00	gold quality
bronchial epithelial cell	CL:0002328	92.25	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.16	gold quality
bronchus	UBERON:0002185	90.91	gold quality
oviduct epithelium	UBERON:0004804	89.29	gold quality
mucosa of paranasal sinus	UBERON:0005030	85.61	gold quality
fallopian tube	UBERON:0003889	79.14	gold quality
epithelium of nasopharynx	UBERON:0001951	72.86	gold quality
nasal cavity mucosa	UBERON:0001826	67.48	gold quality
right lung	UBERON:0002167	61.40	gold quality
caput epididymis	UBERON:0004358	59.52	gold quality
trachea	UBERON:0003126	55.02	gold quality
endometrium	UBERON:0001295	54.41	gold quality
left uterine tube	UBERON:0001303	53.54	gold quality
endothelial cell	CL:0000115	52.11	gold quality
ventricular zone	UBERON:0003053	51.63	silver quality
lung	UBERON:0002048	48.52	gold quality
nasal cavity epithelium	UBERON:0005384	47.81	silver quality
hypothalamus	UBERON:0001898	47.41	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	46.46	silver quality
sural nerve	UBERON:0015488	46.23	silver quality
thymus	UBERON:0002370	45.91	gold quality
upper lobe of lung	UBERON:0008948	45.25	gold quality
caudate nucleus	UBERON:0001873	45.24	gold quality
upper lobe of left lung	UBERON:0008952	44.93	gold quality
Ammon’s horn	UBERON:0001954	44.74	gold quality
endocervix	UBERON:0000458	44.62	gold quality
superior vestibular nucleus	UBERON:0007227	43.92	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting STOML3, 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-340-5P	100.00	72.50	4437
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 1)

• Amplification of the STOML3 gene is associated with mesenchymal differentiation in gliosarcoma. (PMID:22538188)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	stoml3b	ENSDARG00000057035
danio_rerio	stoml3a	ENSDARG00000079914
mus_musculus	Stoml3	ENSMUSG00000027744
rattus_norvegicus	Stoml3	ENSRNOG00000011006
drosophila_melanogaster	CG42540	FBGN0260657
caenorhabditis_elegans		WBGENE00006064

Paralogs (4): STOML1 (ENSG00000067221), NPHS2 (ENSG00000116218), STOM (ENSG00000148175), STOML2 (ENSG00000165283)

Protein

Protein identifiers

Stomatin-like protein 3 — Q8TAV4 (reviewed: Q8TAV4)

All UniProt accessions (1): Q8TAV4

UniProt curated annotations — full annotation on UniProt →

Function. Required for the function of many mechanoreceptors. Modulate mechanotransduction channels and acid-sensing ion channels (ASIC) proteins. Potentiates PIEZO1 and PIEZO2 function by increasing their sensitivity to mechanical stimulations.

Subunit / interactions. Homodimer. Interacts with PIEZO1 and PIEZO2.

Subcellular location. Cell membrane.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q8TAV4-1	1	yes
Q8TAV4-2	2

RefSeq proteins (2): NP_001137505, NP_660329* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001107	Band_7	Domain
IPR001972	Stomatin_HflK_fam	Family
IPR018080	Band_7/stomatin-like_CS	Conserved_site
IPR036013	Band_7/SPFH_dom_sf	Homologous_superfamily
IPR043202	Band-7_stomatin-like	Family

Pfam: PF01145

UniProt features (6 total): modified residue 2, chain 1, transmembrane region 1, topological domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAV4-F1	84.32	0.58

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 (2): 7, 241

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-2672351	Stimuli-sensing channels
R-HSA-382551	Transport of small molecules
R-HSA-983712	Ion channel transport

MSigDB gene sets: 56 (showing top): FREAC2_01, FOXO1_01, chr13q13, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, DANG_BOUND_BY_MYC, FOXO4_02, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, FOXO3_01, REACTOME_STIMULI_SENSING_CHANNELS, REACTOME_TRANSPORT_OF_SMALL_MOLECULES, ZFP3_TARGET_GENES, MIR4659A_3P_MIR4659B_3P, MIR548N, MIR10527_5P

GO Biological Process (1): signal transduction (GO:0007165)

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

GO Cellular Component (5): plasma membrane (GO:0005886), cilium (GO:0005929), neuron projection (GO:0043005), membrane raft (GO:0045121), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Ion channel transport	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
plasma membrane bounded cell projection	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	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
intraciliary transport particle	1
membrane-bounded organelle	1
membrane microdomain	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1494 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STOML3	TRPV1	Q8NER1	807
STOML3	BBS4	Q96RK4	695
STOML3	BBS1	Q8NFJ9	690
STOML3	PIEZO2	Q9H5I5	671
STOML3	PIEZO1	Q92508	667
STOML3	BBS7	Q8IWZ6	649
STOML3	ASIC3	Q9UHC3	596
STOML3	BBS2	Q9BXC9	590
STOML3	TTC8	Q8TAM2	565
STOML3	ASIC2	Q16515	533
STOML3	BBS10	Q8TAM1	533
STOML3	CNGA2	Q16280	512
STOML3	EDN2	P20800	497
STOML3	BBS12	Q6ZW61	497
STOML3	MCHR1	Q99705	491

IntAct

19 interactions, top by confidence:

A	B	Type	Score
UPK2	STOML3	psi-mi:“MI:0915”(physical association)	0.560
CLDN19	STOML3	psi-mi:“MI:0915”(physical association)	0.560
JAGN1	STOML3	psi-mi:“MI:0915”(physical association)	0.560
ADAM33	STOML3	psi-mi:“MI:0915”(physical association)	0.560
ZDHHC24	STOML3	psi-mi:“MI:0915”(physical association)	0.560
STOML3	SEC22A	psi-mi:“MI:0915”(physical association)	0.560
ZDHHC24	STOML3	psi-mi:“MI:0915”(physical association)	0.000
SEC22A	STOML3	psi-mi:“MI:0915”(physical association)	0.000
UPK2	STOML3	psi-mi:“MI:0915”(physical association)	0.000
CLDN19	STOML3	psi-mi:“MI:0915”(physical association)	0.000
JAGN1	STOML3	psi-mi:“MI:0915”(physical association)	0.000
ADAM33	STOML3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): STOML3 (Two-hybrid), STOML3 (Two-hybrid), ADAM33 (Two-hybrid), CLDN19 (Two-hybrid), JAGN1 (Two-hybrid), ZDHHC24 (Two-hybrid), STOML3 (Negative Genetic), STOML3 (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex)

ESM2 similar proteins: A3QMC6, A9UMS3, H1VAN0, H1VPS8, H2FLJ1, O04331, O08917, O13127, O35129, O49460, O60121, O61491, O75477, O75955, O94550, P16148, P24156, P26659, P27105, P40961, P50085, P50093, P54116, P72655, P77306, Q28DX1, Q2HJ97, Q32LL2, Q4FZT0, Q54GI9, Q54Q31, Q5RB19, Q5RBL4, Q5RCJ9, Q5XIH7, Q5ZMN3, Q7YR41, Q8TAV4, Q91X78, Q99623

Diamond homologs: H2FLJ1, O26788, O28852, O59180, O60121, P0AA53, P0AA54, P0AA55, P0AA56, P0DKS0, P27105, P54116, P63694, P72655, P9WPR8, P9WPR9, Q16TM5, Q19200, Q19958, Q27433, Q32LL2, Q4FZT0, Q58237, Q6PE84, Q7PPU9, Q8TAV4, Q99JB2, Q9UJZ1, Q9V0Y1, Q9VZA4, P0ABC7, P0ABC8, P40605, Q20657, Q21190, Q22165, Q5UP73, Q9KV09, Q9UBI4, Q8CI66

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

947 predictions. Top by Δscore:

Variant	Effect	Δscore
13:38967045:AGGAC:A	acceptor_gain	1.0000
13:38967046:GGAC:G	acceptor_gain	1.0000
13:38967047:GAC:G	acceptor_gain	1.0000
13:38967048:AC:A	acceptor_gain	1.0000
13:38967049:CC:C	acceptor_gain	1.0000
13:38967049:CCTGA:C	acceptor_loss	1.0000
13:38967050:C:CC	acceptor_gain	1.0000
13:38967055:A:AC	acceptor_gain	1.0000
13:38967060:A:T	acceptor_gain	1.0000
13:38968395:CTTA:C	donor_loss	1.0000
13:38968396:TTAC:T	donor_loss	1.0000
13:38968397:TACCT:T	donor_loss	1.0000
13:38968398:A:AC	donor_gain	1.0000
13:38968398:A:AT	donor_loss	1.0000
13:38968398:AC:A	donor_gain	1.0000
13:38968399:C:CA	donor_gain	1.0000
13:38968399:CC:C	donor_gain	1.0000
13:38968399:CCT:C	donor_gain	1.0000
13:38968399:CCTT:C	donor_gain	1.0000
13:38968399:CCTTG:C	donor_gain	1.0000
13:38968530:AAAGT:A	acceptor_gain	1.0000
13:38968531:AAGT:A	acceptor_gain	1.0000
13:38968532:AGT:A	acceptor_gain	1.0000
13:38968533:GT:G	acceptor_gain	1.0000
13:38968535:C:CA	acceptor_loss	1.0000
13:38968535:C:CC	acceptor_gain	1.0000
13:38968536:T:G	acceptor_loss	1.0000
13:38968542:C:CT	acceptor_gain	1.0000
13:38968542:C:T	acceptor_gain	1.0000
13:38968543:A:T	acceptor_gain	1.0000

AlphaMissense

1872 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:38968423:C:G	A210P	1.000
13:38967040:C:G	A221P	0.999
13:38968411:C:G	A214P	0.999
13:38968429:C:G	A208P	0.999
13:38967022:C:G	A227P	0.998
13:38968405:C:G	A216P	0.998
13:38968416:C:G	R212P	0.998
13:38968438:C:G	A205P	0.998
13:38970271:C:G	A144P	0.998
13:38976593:C:G	R59P	0.998
13:38968435:C:G	A206P	0.997
13:38968504:C:A	G183W	0.997
13:38970270:G:T	A144D	0.997
13:38970376:C:G	D109H	0.997
13:38966952:A:G	L250P	0.996
13:38966961:A:G	L247P	0.996
13:38967000:G:T	A234D	0.996
13:38967001:C:G	A234P	0.996
13:38967009:A:G	L231P	0.996
13:38967019:A:G	S228P	0.996
13:38970258:A:G	L148P	0.996
13:38970375:T:A	D109V	0.996
13:38966958:C:G	R248P	0.995
13:38966998:A:G	S235P	0.995
13:38968504:C:G	G183R	0.995
13:38968504:C:T	G183R	0.995
13:38968507:A:G	W182R	0.995
13:38968507:A:T	W182R	0.995
13:38970351:C:T	G117E	0.995
13:38970375:T:G	D109A	0.995

dbSNP variants (sampled 300 via entrez): RS1000220299 (13:38974232 C>T), RS1000268875 (13:38980645 C>T), RS1000454134 (13:38986315 A>C), RS1000495020 (13:38975461 T>A), RS1000535114 (13:38972728 C>A,G,T), RS1000558908 (13:38981833 A>G), RS1000611377 (13:38982114 T>C), RS1000781732 (13:38987527 C>G), RS1000975651 (13:38979708 A>C), RS1001026072 (13:38969627 A>C,G), RS1001034225 (13:38969906 T>C,G), RS1001052884 (13:38973119 A>C), RS1001147603 (13:38976046 C>T), RS1001198548 (13:38967954 T>C), RS1001199285 (13:38988696 A>T)

Disease associations

OMIM: gene MIM:608327 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000753_7	Metabolic syndrome	3.000000e-06
GCST003518_90	Daytime sleep phenotypes	5.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0000195	metabolic syndrome
EFO:0004343	waist-hip ratio
EFO:0007828	daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	4
Phenylmercuric Acetate	increases expression, affects cotreatment	2
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Methotrexate	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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