STUM

Summary

STUM (stum, mechanosensory transduction mediator homolog, HGNC:30491) is a protein-coding gene on chromosome 1q42.12, encoding Protein stum homolog (Q69YW2).

Predicted to be located in membrane.

Source: NCBI Gene 375057 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001003665

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30491
Approved symbol	STUM
Name	stum, mechanosensory transduction mediator homolog
Location	1q42.12
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761P211
Ensembl gene	ENSG00000203685
Ensembl biotype	protein_coding
Entrez	375057

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000366788, ENST00000366789, ENST00000467495

RefSeq mRNA: 2 — MANE Select: NM_001003665 NM_001003665, NM_001410930

CCDS: CCDS31044, CCDS91166

Canonical transcript exons

ENST00000366788 — 4 exons

Exon	Start	End
ENSE00001442621	226596802	226596981
ENSE00001899880	226602006	226609230
ENSE00002355625	226600666	226600674
ENSE00003850864	226548764	226549106

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 98.53.

FANTOM5 (CAGE): breadth broad, TPM avg 2.7193 / max 105.0431, expressed in 411 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
8872	2.2778	393
8873	0.2726	107
8871	0.1689	84

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lateral nuclear group of thalamus	UBERON:0002736	98.53	gold quality
sural nerve	UBERON:0015488	97.63	gold quality
pons	UBERON:0000988	94.67	gold quality
amygdala	UBERON:0001876	92.96	gold quality
temporal lobe	UBERON:0001871	91.97	gold quality
CA1 field of hippocampus	UBERON:0003881	91.81	gold quality
orbitofrontal cortex	UBERON:0004167	91.57	gold quality
entorhinal cortex	UBERON:0002728	90.89	gold quality
cortical plate	UBERON:0005343	90.73	gold quality
cingulate cortex	UBERON:0003027	90.06	gold quality
prefrontal cortex	UBERON:0000451	90.05	gold quality
anterior cingulate cortex	UBERON:0009835	89.94	gold quality
Ammon’s horn	UBERON:0001954	89.88	gold quality
Brodmann (1909) area 46	UBERON:0006483	89.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.49	gold quality
dorsal plus ventral thalamus	UBERON:0001897	89.07	gold quality
lateral globus pallidus	UBERON:0002476	89.04	gold quality
frontal cortex	UBERON:0001870	88.26	gold quality
neocortex	UBERON:0001950	87.93	gold quality
caudate nucleus	UBERON:0001873	87.82	gold quality
cerebral cortex	UBERON:0000956	87.81	gold quality
telencephalon	UBERON:0001893	87.47	gold quality
putamen	UBERON:0001874	87.37	gold quality
frontal pole	UBERON:0002795	87.11	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	86.67	gold quality
right frontal lobe	UBERON:0002810	86.59	gold quality
superior frontal gyrus	UBERON:0002661	86.50	gold quality
forebrain	UBERON:0001890	86.26	gold quality
nucleus accumbens	UBERON:0001882	85.74	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.75	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

278 targeting STUM, 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-190A-3P	100.00	80.35	5520
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	stum	ENSDARG00000041915
mus_musculus	Stum	ENSMUSG00000053963
rattus_norvegicus		ENSRNOG00000074432
drosophila_melanogaster	stum	FBGN0050263
caenorhabditis_elegans		WBGENE00021778

Protein

Protein identifiers

Protein stum homolog — Q69YW2 (reviewed: Q69YW2)

All UniProt accessions (2): Q69YW2, F8WD64

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SPEC3 family. Stum subfamily.

RefSeq proteins (2): NP_001003665, NP_001397859 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026673	SPEC3/Stum	Family

Pfam: PF15795

UniProt features (4 total): transmembrane region 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q69YW2-F1	60.03	0.00

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): 26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, PEDRIOLI_MIR31_TARGETS_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, RAPA_EARLY_UP.V1_UP, PRC1_BMI_UP.V1_UP, DACH1_TARGET_GENES, RYBP_TARGET_GENES, SIX1_TARGET_GENES, ZNF2_TARGET_GENES, ZNF23_TARGET_GENES, ZNF30_TARGET_GENES, ZNF329_TARGET_GENES, ZNF33A_TARGET_GENES, ZNF528_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

164 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STUM	LYSMD4	Q5XG99	507
STUM	ENTREP2	O60320	447
STUM	UBE2U	Q5VVX9	415
STUM	UBFD1	O14562	403
STUM	LRRC55	Q6ZSA7	390
STUM	DOK6	Q6PKX4	377
STUM	CWH43	Q9H720	368
STUM	PNLDC1	Q8NA58	360
STUM	CPNE7	Q9UBL6	355
STUM	CDYL2	Q8N8U2	348
STUM	ARHGAP39	Q9C0H5	348
STUM	LPGAT1	Q92604	311
STUM	SIGLEC11	Q96RL6	311
STUM	TNIP3	Q96KP6	300
STUM	IL1RAPL2	Q9NP60	300

IntAct

6 interactions, top by confidence:

A	B	Type	Score
ZDHHC24	STUM	psi-mi:“MI:0915”(physical association)	0.560
STUM	ZDHHC24	psi-mi:“MI:0915”(physical association)	0.560
STUM	PLSCR1	psi-mi:“MI:0914”(association)	0.350
MFSD3	NME4	psi-mi:“MI:0914”(association)	0.350

BioGRID (21): C4orf32 (Affinity Capture-MS), HSDL1 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), APOB (Affinity Capture-MS), COX6B1 (Affinity Capture-MS), GPRC5B (Affinity Capture-MS), NDUFS4 (Affinity Capture-MS), GK (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), SOAT1 (Affinity Capture-MS), PLSCR1 (Affinity Capture-MS), TMEM245 (Affinity Capture-MS), PIEZO1 (Affinity Capture-MS), ATP6V0A2 (Affinity Capture-MS), DOLK (Affinity Capture-MS)

ESM2 similar proteins: A1L4L8, A2YMP7, A5D992, B4FF80, B4FUS3, B6SGC5, B6SJQ0, B6TYV8, B6TZ45, D1ZIW5, D4AT37, D9HP19, D9HP20, D9HP23, D9HP25, D9HP26, D9HP27, O43609, P0CW97, P0CW98, Q08EJ0, Q0VBF8, Q1L0X2, Q28793, Q2TBG9, Q5BJH7, Q5Y171, Q69YW2, Q6NYK3, Q6PEC3, Q75IC7, Q7SAJ6, Q8H5X5, Q8L7E9, Q8L9S1, Q8S8T8, Q91049, Q94CD4, Q9BT67, Q9LQU2

Diamond homologs: P16537, Q0VBF8, Q5TYP8, Q69YW2, Q9W2E1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1174 predictions. Top by Δscore:

Variant	Effect	Δscore
1:226596977:TGCCA:T	donor_gain	1.0000
1:226596978:GCCA:G	donor_gain	1.0000
1:226596978:GCCAG:G	donor_gain	1.0000
1:226596979:CCAG:C	donor_loss	1.0000
1:226596980:CA:C	donor_gain	1.0000
1:226596980:CAGTG:C	donor_loss	1.0000
1:226596982:G:GG	donor_gain	1.0000
1:226596982:G:T	donor_loss	1.0000
1:226596983:T:A	donor_loss	1.0000
1:226549105:GG:G	donor_gain	0.9900
1:226549106:GG:G	donor_gain	0.9900
1:226549106:GGTAA:G	donor_loss	0.9900
1:226549107:G:GG	donor_gain	0.9900
1:226549107:GTA:G	donor_loss	0.9900
1:226549108:T:G	donor_loss	0.9900
1:226596979:CCA:C	donor_gain	0.9900
1:226596984:GAG:G	donor_loss	0.9900
1:226596985:AGT:A	donor_loss	0.9900
1:226602111:G:GT	donor_gain	0.9900
1:226550140:TTCC:T	donor_gain	0.9800
1:226596799:CA:C	acceptor_loss	0.9800
1:226596800:A:AC	acceptor_loss	0.9800
1:226596801:GGGAC:G	acceptor_gain	0.9800
1:226549100:GGAC:G	donor_gain	0.9700
1:226596800:A:AG	acceptor_gain	0.9700
1:226596800:AG:A	acceptor_gain	0.9700
1:226596801:G:GG	acceptor_gain	0.9700
1:226596801:GG:G	acceptor_gain	0.9700
1:226596985:A:AG	donor_gain	0.9700
1:226596986:G:GG	donor_gain	0.9700

AlphaMissense

914 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:226549044:C:A	P47H	1.000
1:226549065:C:A	A54D	1.000
1:226549068:T:A	V55D	1.000
1:226549073:T:C	C57R	1.000
1:226549087:C:A	N61K	1.000
1:226549087:C:G	N61K	1.000
1:226549098:C:A	P65Q	1.000
1:226549101:G:A	G66E	1.000
1:226549106:G:A	G68R	1.000
1:226549106:G:C	G68R	1.000
1:226596802:G:A	G68E	1.000
1:226596933:G:C	G112R	1.000
1:226596934:G:A	G112D	1.000
1:226596934:G:T	G112V	1.000
1:226596936:T:A	W113R	1.000
1:226596936:T:C	W113R	1.000
1:226596945:A:C	S116R	1.000
1:226596946:G:T	S116I	1.000
1:226596947:C:A	S116R	1.000
1:226596947:C:G	S116R	1.000
1:226596954:T:A	W119R	1.000
1:226596954:T:C	W119R	1.000
1:226596956:G:C	W119C	1.000
1:226596956:G:T	W119C	1.000
1:226596957:G:C	G120R	1.000
1:226596958:G:A	G120D	1.000
1:226596958:G:T	G120V	1.000
1:226549038:C:A	A45D	0.999
1:226549041:T:A	I46N	0.999
1:226549043:C:T	P47S	0.999

dbSNP variants (sampled 300 via entrez): RS1000063416 (1:226595862 C>T), RS1000175762 (1:226599578 G>A), RS1000215311 (1:226559498 A>G), RS1000247531 (1:226600033 G>A), RS1000327298 (1:226553732 G>A), RS1000331375 (1:226574295 T>C), RS1000340104 (1:226571396 C>T), RS1000457692 (1:226568216 T>C), RS1000489447 (1:226605505 G>A), RS1000511451 (1:226601356 A>G), RS1000567451 (1:226559181 G>A,C), RS1000653523 (1:226554948 G>A), RS1000654464 (1:226561731 A>C), RS1000663584 (1:226555254 A>G), RS1000667701 (1:226594572 G>C)

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

2 associations (top):

Study	Trait	p-value
GCST005094_1	Iris color (L* coordinate)	8.000000e-06
GCST005689_2	Major depressive disorder (unexposed to adversity)	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0003949	eye color

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
Aflatoxin B1	decreases methylation	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
propionaldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
tebuconazole	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
Amiodarone	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases expression, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Nickel	decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1
Triclosan	decreases expression	1
Valproic Acid	increases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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