SELENBP1

Summary

SELENBP1 (selenium binding protein 1, HGNC:10719) is a protein-coding gene on chromosome 1q21.3, encoding Methanethiol oxidase (Q13228). Catalyzes the oxidation of methanethiol, an organosulfur compound known to be produced in substantial amounts by gut bacteria.

This gene encodes a member of the selenium-binding protein family. Selenium is an essential nutrient that exhibits potent anticarcinogenic properties, and deficiency of selenium may cause certain neurologic diseases. The effects of selenium in preventing cancer and neurologic diseases may be mediated by selenium-binding proteins, and decreased expression of this gene may be associated with several types of cancer. The encoded protein may play a selenium-dependent role in ubiquitination/deubiquitination-mediated protein degradation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 8991 — RefSeq curated summary.

At a glance

• Gene–disease (curated): extraoral halitosis due to methanethiol oxidase deficiency (Strong, GenCC) — +2 more curated relationships
• GWAS associations: 3
• Clinical variants (ClinVar): 124 total — 2 pathogenic, 3 likely-pathogenic
• Phenotypes (HPO): 5
• MANE Select transcript: NM_003944

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10719
Approved symbol	SELENBP1
Name	selenium binding protein 1
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	hSP56, hSBP, LPSB
Ensembl gene	ENSG00000143416
Ensembl biotype	protein_coding
OMIM	604188
Entrez	8991

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 25 protein_coding, 6 retained_intron, 5 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000368868, ENST00000423070, ENST00000424475, ENST00000426705, ENST00000427867, ENST00000427977, ENST00000443708, ENST00000447402, ENST00000455397, ENST00000455839, ENST00000458566, ENST00000463664, ENST00000465273, ENST00000470345, ENST00000473693, ENST00000474352, ENST00000492643, ENST00000493560, ENST00000498494, ENST00000896522, ENST00000896523, ENST00000896524, ENST00000896525, ENST00000896526, ENST00000896527, ENST00000896528, ENST00000896529, ENST00000896530, ENST00000896531, ENST00000896532, ENST00000896533, ENST00000935723, ENST00000935724, ENST00000966378, ENST00000966379, ENST00000966380, ENST00000966381, ENST00000966382

RefSeq mRNA: 3 — MANE Select: NM_003944 NM_001258288, NM_001258289, NM_003944

CCDS: CCDS58027, CCDS60266, CCDS995

Canonical transcript exons

ENST00000368868 — 12 exons

Exon	Start	End
ENSE00001842664	151364304	151364705
ENSE00003479088	151366722	151366904
ENSE00003513345	151372638	151372705
ENSE00003541897	151369004	151369189
ENSE00003594795	151369713	151369769
ENSE00003606631	151368199	151368319
ENSE00003612172	151369442	151369554
ENSE00003612748	151365563	151365684
ENSE00003642312	151364926	151365044
ENSE00003649409	151365189	151365281
ENSE00003661887	151366275	151366453
ENSE00003695602	151365768	151365846

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 99.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.9321 / max 1674.0747, expressed in 1325 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14436	34.1756	1323
14435	1.7565	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	99.92	gold quality
rectum	UBERON:0001052	99.54	gold quality
colonic mucosa	UBERON:0000317	99.49	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.46	gold quality
right uterine tube	UBERON:0001302	99.35	gold quality
transverse colon	UBERON:0001157	99.33	gold quality
right lobe of thyroid gland	UBERON:0001119	99.03	gold quality
right lobe of liver	UBERON:0001114	98.95	gold quality
left lobe of thyroid gland	UBERON:0001120	98.90	gold quality
thyroid gland	UBERON:0002046	98.82	gold quality
body of stomach	UBERON:0001161	98.65	gold quality
large intestine	UBERON:0000059	98.38	gold quality
colon	UBERON:0001155	98.36	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	98.34	gold quality
fundus of stomach	UBERON:0001160	98.18	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.17	gold quality
ileal mucosa	UBERON:0000331	98.15	gold quality
nasal cavity epithelium	UBERON:0005384	98.08	gold quality
right lung	UBERON:0002167	98.03	gold quality
intestine	UBERON:0000160	97.94	gold quality
trabecular bone tissue	UBERON:0002483	97.94	gold quality
sigmoid colon	UBERON:0001159	97.91	gold quality
epithelium of bronchus	UBERON:0002031	97.88	gold quality
mucosa of stomach	UBERON:0001199	97.86	gold quality
bronchus	UBERON:0002185	97.82	gold quality
stomach	UBERON:0000945	97.76	gold quality
liver	UBERON:0002107	97.76	gold quality
left uterine tube	UBERON:0001303	97.74	gold quality
upper lobe of left lung	UBERON:0008952	97.73	gold quality
bronchial epithelial cell	CL:0002328	97.70	gold quality

Single-cell (SCXA)

Detected in 16 experiment(s), a significant marker in 14.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	935.36
E-MTAB-9067	yes	766.82
E-HCAD-1	yes	83.07
E-CURD-112	yes	70.91
E-MTAB-10042	yes	55.19
E-MTAB-6701	yes	53.65
E-CURD-114	yes	44.88
E-MTAB-9221	yes	27.31
E-GEOD-130148	yes	18.32
E-MTAB-8410	yes	16.05
E-MTAB-9388	yes	9.12
E-HCAD-9	yes	8.14
E-HCAD-10	yes	6.22
E-CURD-98	no	800.07
E-MTAB-9467	no	2.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting SELENBP1, 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-6748-5P	100.00	65.81	1057
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-7843-3P	98.31	67.94	803
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-4468	98.01	66.85	1187
HSA-MIR-6787-3P	97.75	66.17	1233
HSA-MIR-3085-5P	97.72	65.43	544
HSA-MIR-7160-3P	96.40	64.15	462
HSA-MIR-6823-5P	96.26	65.69	919
HSA-MIR-3162-5P	95.67	67.53	794

Literature-anchored findings (GeneRIF, showing 40)

• SBP may be involved in the initial sequential events in rapid cell outgrowth, such as determining direction of cell outgrowth and recruitment of actin monomer. (PMID:15108003)
• changes of SELENBP1 expression in malignant ovarian cancer are an indicator of aberration of selenium/androgen pathways and may reveal prognostic information of ovarian cancer (PMID:16380993)
• Suppression of SELENBP1 is a frequent and late event in colorectal carcinogenesis, and may contribute to the rapid progression of colorectal carcinoma. (PMID:16645984)
• Elevated SELENBP1 is a possibly consistent feature in the schizophrenic brain and this could underlie some commonalities of psychosis across the boundaries of diagnoses. (PMID:18163446)
• Associated with differentiation of the normal colonic epithelia and may be a positive prognostic factor for survival in stage III colorectal carcinoma (PMID:18435490)
• VDU1 was identified as a protein partner of hSP56. (PMID:19118533)
• The genetic variation in SELENBP1 may influence risk for the disorder, while this significance did not remain when other inheritance models were considered. (PMID:19596560)
• loss of selenium-binding protein 1 associated with increasing epithelial proliferation indicates selenium-binding protein 1 is involved in tumorigenesis of ovarian and micropapillary serous borderline tumor and low-grade serous carcinoma. (PMID:19896693)
• SBP1 has tumor suppressor functions that are inhibited in colorectal cancer through epigenetic silencing (PMID:19924303)
• SELENBP1 expression may be an important predictor of response to chemoprevention or chemosensitization with certain forms of selenium in esophageal tissues. (PMID:20332323)
• down-regulation of SBP1 may play a key role in the tumorigenic process of human gastric carcinoma (PMID:20354826)
• The suppression of Selenium-binding protein 1 may be a late event in gastric carcinogenesis. (PMID:20480265)
• SP1 is present in reduced levels in several cancer types as compared with normal tissues, and lower levels are associated with poor clinical prognosis. (PMID:20530237)
• evidence for recurrence of decreased copy-number of the SELENBP1 locus in three unrelated schizophrenia patients’ cohorts but not in controls, raising the possibility of functional involvement of these mutations in the etiology of the disease (PMID:20615253)
• Decreased expression of selenium-binding protein 1 in uterine leiomyoma may indicate a role of the protein in tumorigenesis. (PMID:21143902)
• A reduced SELENBP1 expression by immunohistochemistry in liver tissues of patients with hepatocarcinoma (HCC), is reported. (PMID:21338716)
• The 3-year survival rate of gastric cancer patients with high expression of selenium-binding protein 1 was significantly higher than that of patients with low expression (PMID:21497372)
• Glutathione peroxidase (GPx)-1 enzyme activity is inversely correlated with selenium binding protein (SBP)-1 levels in prostate tissue, based on the Gleason score. (PMID:22072582)
• The expression level of SELENBP1 could be an important marker for predicting survival and effectiveness of selenium supplementation in breast cancer. (PMID:23704933)
• Decreased SELENBP1 expression is an early event in lung squamous cell cancer tumorigenesis. (PMID:23977169)
• the downregulated SELENBP1 expression was reactivated by inducing differentiation. Therefore, SELENBP1 is a potential pharmacological target for individualized CRC treatment. (PMID:24737289)
• hSP56 plays an important role in regulating HIF-1alpha, which may be one of mechanisms of hSP56 expression in suppressing the malignant characteristics of prostate cancer cells. (PMID:24874852)
• Decreased selenium-binding protein 1 mRNA expression is associated with renal cell carcinoma. (PMID:25227434)
• These results have revealed a novel mechanism that SELENBP1-mediated cancer inhibition is through altering lipid/glucose metabolic signaling pathways. (PMID:25974208)
• Data indicate that loss of SBP1 may play an independent contributing role in prostate cancer progression and its levels might be useful in distinguishing indolent from aggressive disease. (PMID:25993660)
• elevated transcript expression is widespread throughout the prefrontal cortex in schizophrenia (PMID:26241353)
• cysteine 57 is a critical determinant of SBP1 function and may play a significant role in mitochondrial function. (PMID:26593911)
• Downregulation of selenium-binding protein 1 is associated with lung squamous cell carcinoma. (PMID:26956891)
• High anti-SBP1 is associated with infertile women with premature ovarian failure. (PMID:27965399)
• Mutations in SELENBP1, encoding a methanethiol oxidase, cause extraoral halitosis. (PMID:29255262)
• Data demonstrate that Selenbp1 is a direct target of Nkx2-1, which inhibits lung adenocarcinoma growth in vivo. Selenbp1 is an important suppressor of lung tumor growth that functions in a positive feedback loop with Nkx2-1, and whose loss is associated with worse patient outcome. (PMID:30002193)
• the transcriptional regulation of SBP1, the different physiological roles reported for SBP1, as well as the implications of SBP1 function in cancer and other diseases are presented. (PMID:30400135)
• data indicate that SELENBP1 constitutes a circulating biomarker for cardiac events categorizing patients with suspected acute coronary syndrome at first medical contact into high-risk or low-risk for major adverse cardiac events and death, independent from and complimentary to current biomarkers (PMID:30732890)
• oxidative stress-induced DNA methylation of miR-122 aggravates colitis targeting SELENBP1 partially by p65NF-kappaB signaling and may promote the progression of Crohn’s disease. (PMID:31019652)
• Increased concentrations of Selenbp1 reflected the duration of ischemia and myocardial damage during cardiac surgical procedures, and reliably identifiesd patients at risk of adverse outcomes. (PMID:31450690)
• Selenium-binding protein 1 transcriptionally activates p21 expression via p53-independent mechanism and its frequent reduction associates with poor prognosis in bladder cancer. (PMID:31918717)
• Hepatitis B Virus-X Downregulates Expression of Selenium Binding Protein 1. (PMID:32443734)
• Selenium-binding protein 1 alters energy metabolism in prostate cancer cells. (PMID:32511787)
• A coupled enzyme assay for detection of selenium-binding protein 1 (SELENBP1) methanethiol oxidase (MTO) activity in mature enterocytes. (PMID:33901808)
• Downregulation of SELENBP1 enhances oral squamous cell carcinoma chemoresistance through KEAP1-NRF2 signaling. (PMID:33907880)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	selenbp1	ENSDARG00000024717
mus_musculus	Selenbp1	ENSMUSG00000068874
mus_musculus	Selenbp2	ENSMUSG00000068877
rattus_norvegicus	Selenbp1	ENSRNOG00000047158
drosophila_melanogaster	CG7966	FBGN0038115
caenorhabditis_elegans		WBGENE00011249
caenorhabditis_elegans		WBGENE00012538

Protein

Protein identifiers

Methanethiol oxidase — Q13228 (reviewed: Q13228)

Alternative names: 56 kDa selenium-binding protein, Selenium-binding protein 1

All UniProt accessions (8): Q13228, A6PVX1, C9JVL0, F2Z2W8, F8WBA9, F8WCR4, H0Y532, V9HWG1

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the oxidation of methanethiol, an organosulfur compound known to be produced in substantial amounts by gut bacteria. Selenium-binding protein which may be involved in the sensing of reactive xenobiotics in the cytoplasm. May be involved in intra-Golgi protein transport.

Subunit / interactions. Interacts with USP33.

Subcellular location. Nucleus. Cytoplasm. Cytosol. Membrane.

Tissue specificity. Widely expressed. Highly expressed in liver, lung, colon, prostate, kidney and pancreas. In brain, present both in neurons and glia (at protein level). Down-regulated in lung adenocarcinoma, colorectal carcinoma and ovarian cancer. Two-fold up-regulated in brain and blood from schizophrenia patients.

Post-translational modifications. Phosphorylated. The N-terminus is blocked.

Disease relevance. Extraoral halitosis due to methanethiol oxidase deficiency (EHMTO) [MIM:618148] An autosomal recessive malodor condition characterized by extraoral blood-borne halitosis resulting from the accumulation of sulfur-containing metabolites. In extraoral blood-borne halitosis, malodorant compounds are carried to the lungs, where they enter the breath. Affected individuals have a cabbage-like breath odor, high levels of methanethiol and dimethylsulfide in oral and nasal breath, and elevated urinary excretion of dimethylsulfoxide in the absence of intake of dimethylsulfide-containing food or use of sulfur-containing medication, lower-gastrointestinal problems, and known metabolic defects, such as methionine adenosyltransferase deficiency and tyrosinemia. The disease is caused by variants affecting the gene represented in this entry.

Induction. Down-regulated by androgen in prostate cancer cells.

Pathway. Organosulfur degradation.

Similarity. Belongs to the selenium-binding protein family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q13228-1	1	yes
Q13228-2	2
Q13228-3	3
Q13228-4	4

RefSeq proteins (3): NP_001245217, NP_001245218, NP_003935* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008826	Se-bd	Family

Pfam: PF05694

Catalyzed reactions (Rhea), 1 shown:

• methanethiol + O2 + H2O = hydrogen sulfide + formaldehyde + H2O2 + H(+) (RHEA:11812)

UniProt features (23 total): sequence conflict 11, modified residue 4, sequence variant 3, splice variant 3, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13228-F1	96.85	0.97

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 (4): 2, 111, 371, 467

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 210 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, KOBAYASHI_EGFR_SIGNALING_24HR_UP, GOZGIT_ESR1_TARGETS_DN, LUCAS_HNF4A_TARGETS_UP, LEE_LIVER_CANCER_CIPROFIBRATE_DN, GNF2_ANK1, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, GROSS_HYPOXIA_VIA_HIF1A_DN, GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, MODULE_213, GNF2_SPTA1, LEE_LIVER_CANCER_DENA_DN, GNF2_PCAF

GO Biological Process (1): protein transport (GO:0015031)

GO Molecular Function (4): selenium binding (GO:0008430), methanethiol oxidase activity (GO:0018549), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (8): fibrillar center (GO:0001650), obsolete extracellular space (GO:0005615), nucleolus (GO:0005730), cytosol (GO:0005829), membrane (GO:0016020), extracellular exosome (GO:0070062), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
transport	1
intracellular protein localization	1
establishment of protein localization	1
small molecule binding	1
oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor	1
binding	1
catalytic activity	1
nucleolus	1
nuclear lumen	1
intracellular membraneless organelle	1
cytoplasm	1
extracellular vesicle	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1362 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SELENBP1	ENO1	P06733	751
SELENBP1	SELENOP	P49908	635
SELENBP1	USP1	O94782	535
SELENBP1	TP53	P04637	479
SELENBP1	HSP90AB1	P08238	468
SELENBP1	HIF1A	Q16665	468
SELENBP1	DCAF12	Q5T6F0	462
SELENBP1	HSP90AA1	P07900	457
SELENBP1	ZP2	Q05996	451
SELENBP1	LEP	P41159	446
SELENBP1	A2M	P01023	444
SELENBP1	HSPA4	P34932	441
SELENBP1	KRT84	Q9NSB2	426
SELENBP1	AKR1B10	O60218	425
SELENBP1	FKBP4	Q02790	421

IntAct

106 interactions, top by confidence:

A	B	Type	Score
TRIP13	SELENBP1	psi-mi:“MI:0915”(physical association)	0.800
SELENBP1	TRIP13	psi-mi:“MI:0915”(physical association)	0.800
OAZ3	AZIN1	psi-mi:“MI:0914”(association)	0.800
KIF3A	KIF3C	psi-mi:“MI:0914”(association)	0.730
POLR2J	POLR2D	psi-mi:“MI:0914”(association)	0.730
CTSV	CTSL	psi-mi:“MI:0914”(association)	0.720
ANXA9	PPL	psi-mi:“MI:0914”(association)	0.660
SELENBP1	USP33	psi-mi:“MI:0407”(direct interaction)	0.650
SELENBP1	USP33	psi-mi:“MI:0403”(colocalization)	0.650
SELENBP1	USP33	psi-mi:“MI:0915”(physical association)	0.650
USP33	SELENBP1	psi-mi:“MI:0915”(physical association)	0.650
CAPZA2	CNOT1	psi-mi:“MI:0914”(association)	0.640
SELENBP1	THAP12	psi-mi:“MI:0915”(physical association)	0.560
THAP12	SELENBP1	psi-mi:“MI:0915”(physical association)	0.560
SELENBP1	MSRA	psi-mi:“MI:0915”(physical association)	0.560
SELENBP1	MED31	psi-mi:“MI:0915”(physical association)	0.550
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
MAS1	POTEF	psi-mi:“MI:0914”(association)	0.530
GDF5	SERPINB7	psi-mi:“MI:0914”(association)	0.530
HEATR1	DUSP14	psi-mi:“MI:0914”(association)	0.530
LACC1	DUSP14	psi-mi:“MI:0914”(association)	0.530
FBXL4	DUSP14	psi-mi:“MI:0914”(association)	0.530
NSMAF	DUSP14	psi-mi:“MI:0914”(association)	0.530
FLYWCH2	BAG4	psi-mi:“MI:0914”(association)	0.530
DOLPP1	VSIG8	psi-mi:“MI:0914”(association)	0.530
FNTB	YKT6	psi-mi:“MI:0914”(association)	0.530

BioGRID (195): SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS), TRIP13 (Two-hybrid), DUT (Co-fractionation), FAM49B (Co-fractionation)

ESM2 similar proteins: A2VCW9, A2YGP6, A8E657, A8XKT0, A9RBS1, F4JVN6, O17732, O23264, O42130, O42131, O64459, O80585, P12628, P17563, P22178, P34105, P36428, P36444, P37223, P43279, P51615, Q01320, Q13228, Q2KJ32, Q43772, Q52KZ7, Q569D5, Q5RF48, Q5Z8Y4, Q60HE5, Q63836, Q64399, Q64511, Q6DCH7, Q6ESI7, Q6NUA1, Q6PHD9, Q75HE6, Q8RX87, Q8VIF7

Diamond homologs: A8X2U9, O23264, P17563, Q13228, Q21950, Q2KJ32, Q52KZ7, Q569D5, Q5RF48, Q63836, Q6DCH7, Q6PHD9, Q8VIF7, Q93WN0, Q9LK38

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	3
Uncertain significance	75
Likely benign	8
Benign	8

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
3247711	NC_000001.10:g.(?151314662)(151666077_?)del	Pathogenic
585260	NM_003944.4(SELENBP1):c.481+1G>A	Pathogenic
549486	NM_003944.4(SELENBP1):c.673G>T (p.Gly225Trp)	Likely pathogenic
549495	NM_003944.4(SELENBP1):c.1039G>T (p.Gly347Ter)	Likely pathogenic
549497	NM_003944.4(SELENBP1):c.985C>T (p.His329Tyr)	Likely pathogenic

SpliceAI

1974 predictions. Top by Δscore:

Variant	Effect	Δscore
1:151364920:TCTCA:T	donor_loss	1.0000
1:151364921:CTCAC:C	donor_loss	1.0000
1:151364922:TCAC:T	donor_loss	1.0000
1:151364923:CAC:C	donor_loss	1.0000
1:151364924:A:AG	donor_loss	1.0000
1:151365040:TTTCC:T	acceptor_gain	1.0000
1:151365041:TTCC:T	acceptor_gain	1.0000
1:151365042:TCC:T	acceptor_gain	1.0000
1:151365042:TCCC:T	acceptor_loss	1.0000
1:151365043:CC:C	acceptor_gain	1.0000
1:151365043:CCC:C	acceptor_gain	1.0000
1:151365044:CCT:C	acceptor_gain	1.0000
1:151365045:C:CC	acceptor_gain	1.0000
1:151365045:C:T	acceptor_gain	1.0000
1:151365046:T:A	acceptor_loss	1.0000
1:151365046:T:C	acceptor_gain	1.0000
1:151365046:T:TC	acceptor_gain	1.0000
1:151365056:C:CT	acceptor_gain	1.0000
1:151365183:TCTTA:T	donor_loss	1.0000
1:151365184:CTTA:C	donor_loss	1.0000
1:151365185:TTAC:T	donor_loss	1.0000
1:151365186:TA:T	donor_loss	1.0000
1:151365187:A:C	donor_loss	1.0000
1:151365188:C:CA	donor_loss	1.0000
1:151365524:T:A	donor_gain	1.0000
1:151365528:T:A	donor_gain	1.0000
1:151365532:T:TA	donor_gain	1.0000
1:151365545:T:TA	donor_gain	1.0000
1:151365566:T:TA	donor_gain	1.0000
1:151365604:A:AC	donor_gain	1.0000

AlphaMissense

3075 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:151369135:A:G	W77R	0.999
1:151369135:A:T	W77R	0.999
1:151364954:C:G	D410H	0.998
1:151365003:G:C	S393R	0.998
1:151365003:G:T	S393R	0.998
1:151365005:T:G	S393R	0.998
1:151368230:G:C	S150R	0.998
1:151368230:G:T	S150R	0.998
1:151368232:T:G	S150R	0.998
1:151368262:G:C	H140D	0.998
1:151369147:G:C	H73D	0.998
1:151364561:G:C	S467R	0.997
1:151364561:G:T	S467R	0.997
1:151364563:T:G	S467R	0.997
1:151364568:T:A	D465V	0.997
1:151364569:C:G	D465H	0.997
1:151364957:A:G	W409R	0.997
1:151364957:A:T	W409R	0.997
1:151365651:T:A	D319V	0.997
1:151366349:G:C	H257D	0.997
1:151366783:G:C	S201R	0.997
1:151366783:G:T	S201R	0.997
1:151366785:T:G	S201R	0.997
1:151366816:G:C	F190L	0.997
1:151366816:G:T	F190L	0.997
1:151366818:A:G	F190L	0.997
1:151366820:T:A	D189V	0.997
1:151368271:G:C	H137D	0.997
1:151369056:C:G	R103P	0.997
1:151369133:C:A	W77C	0.997

dbSNP variants (sampled 300 via entrez): RS1000890101 (1:151370871 G>T), RS1000965504 (1:151370041 G>A), RS1001789655 (1:151366011 G>A,C,T), RS1001937682 (1:151371760 C>A,G,T), RS1001991988 (1:151371275 G>A), RS1002146076 (1:151373149 C>A), RS1003672616 (1:151366906 T>C), RS1003691362 (1:151367952 G>A), RS1004180921 (1:151373450 G>C), RS1004334187 (1:151367451 G>A), RS1004462649 (1:151373258 T>A), RS1004686511 (1:151367658 T>C), RS1005281997 (1:151368897 G>A,C), RS1005406936 (1:151365390 G>A,T), RS1005448232 (1:151374374 G>C)

Disease associations

OMIM: gene MIM:604188 | disease phenotypes: MIM:618148

GenCC curated gene-disease

Disease	Classification	Inheritance
extraoral halitosis due to methanethiol oxidase deficiency	Strong	Autosomal recessive
autosomal recessive extra-oral halitosis	Supportive	Autosomal recessive
schizophrenia	No Known Disease Relationship	Unknown

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
extraoral halitosis due to methanethiol oxidase deficiency	Moderate	AR

Mondo (4): extraoral halitosis due to methanethiol oxidase deficiency (MONDO:0029144), Dravet syndrome (MONDO:0100135), schizophrenia (MONDO:0005090), (MONDO:0034186)

Orphanet (2): Dravet syndrome (Orphanet:33069), Autosomal recessive extra-oral halitosis (Orphanet:562538)

HPO phenotypes

5 total (5 of 5 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0003577	Congenital onset
HP:0003593	Infantile onset
HP:0025708	Early young adult onset
HP:0100812	Halitosis

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002041_2	Blood trace element (Cu levels)	3.000000e-20
GCST90002388_626	Lymphocyte count	5.000000e-09
GCST90002404_425	Red cell distribution width	3.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005267	serum copper measurement
EFO:0004587	lymphocyte count
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

92 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, affects expression	5
Air Pollutants	increases oxidation, increases expression, decreases expression, affects cotreatment, increases abundance	5
Estradiol	affects cotreatment, decreases expression	5
sodium arsenite	decreases expression, increases expression	4
Valproic Acid	affects expression, decreases expression, increases methylation	4
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
Tobacco Smoke Pollution	affects expression, decreases expression	3
Cyclosporine	decreases expression	3
Aflatoxin B1	affects expression, decreases expression	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
bisphenol S	decreases expression, increases expression	2
Cadmium	decreases reaction, increases abundance, increases palmitoylation, increases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	decreases expression	2
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	2
Cadmium Chloride	decreases reaction, increases abundance, increases palmitoylation, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
TAK-243	increases sumoylation	1
hempseed oil	affects cotreatment, increases secretion	1
bufotalin	decreases expression	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
methylmercaptan	increases metabolic processing	1
alpha phellandrene	increases expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
lead acetate	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2EY	Abcam HeLa SELENBP1 KO	Cancer cell line	Female
CVCL_D9WK	Ubigene HT-29 SELENBP1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00000374	PHASE4	COMPLETED	Treatment for First-Episode Schizophrenia
NCT00001656	PHASE4	COMPLETED	Comparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774	PHASE4	COMPLETED	To Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001	PHASE4	COMPLETED	CATIE- Schizophrenia Trial
NCT00018668	PHASE4	COMPLETED	Antipsychotic Response in Schizophrenia
NCT00034801	PHASE4	COMPLETED	Olanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905	PHASE4	COMPLETED	A Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088	PHASE4	COMPLETED	Olanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187	PHASE4	COMPLETED	The Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655	PHASE4	COMPLETED	Switching Medication to Treat Schizophrenia
NCT00048828	PHASE4	COMPLETED	Treating Drug-Resistant Childhood Schizophrenia
NCT00053703	PHASE4	COMPLETED	Treatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498	PHASE4	COMPLETED	Risperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802	PHASE4	COMPLETED	Efficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327	PHASE4	COMPLETED	Study of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049	PHASE4	COMPLETED	Study of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012	PHASE4	COMPLETED	Comparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776	PHASE4	COMPLETED	Efficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571	PHASE4	COMPLETED	Olanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368	PHASE4	COMPLETED	The Effects of Risperidone and Olanzapine on Thinking
NCT00114595	PHASE4	COMPLETED	Ethyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923	PHASE4	COMPLETED	Risperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020	PHASE4	COMPLETED	Clinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166	PHASE4	COMPLETED	Treatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847	PHASE4	COMPLETED	Naltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564	PHASE4	COMPLETED	Energy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715	PHASE4	COMPLETED	Efficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223	PHASE4	COMPLETED	Effectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081	PHASE4	COMPLETED	One Year Drug Treatment in First-Episode Schizophrenia
NCT00159120	PHASE4	COMPLETED	Maintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133	PHASE4	COMPLETED	Prodrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757	PHASE4	TERMINATED	12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817	PHASE4	COMPLETED	Effect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026	PHASE4	TERMINATED	Alcoholism and Schizophrenia: Effects of Clozapine
NCT00169039	PHASE4	TERMINATED	Clozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065	PHASE4	COMPLETED	Effectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091	PHASE4	TERMINATED	Clozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423	PHASE4	COMPLETED	Efficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436	PHASE4	COMPLETED	Atomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008	PHASE4	COMPLETED	Aripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety