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GeneBe

SELENBP1

selenium binding protein 1

Basic information

Region (hg38): 1:151364303-151372707

Links

ENSG00000143416NCBI:8991OMIM:604188HGNC:10719Uniprot:Q13228AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
  • extraoral halitosis due to methanethiol oxidase deficiency (Limited), mode of inheritance: AR
  • autosomal recessive extra-oral halitosis (Supportive), mode of inheritance: AR
  • extraoral halitosis due to methanethiol oxidase deficiency (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Extraoral halitosis due to methanethiol oxidase deficiencyARGeneralThe clinical relevance is unclearBiochemical29255262

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SELENBP1 gene.

  • Inborn genetic diseases (23 variants)
  • Extra oral halitosis (3 variants)
  • not provided (3 variants)
  • Extraoral halitosis due to methanethiol oxidase deficiency (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELENBP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
2
clinvar
23
clinvar
1
clinvar
26
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
1
Total 0 3 23 0 2

Highest pathogenic variant AF is 0.0000197

Variants in SELENBP1

This is a list of pathogenic ClinVar variants found in the SELENBP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-151364569-C-T not specified Uncertain significance (Dec 20, 2023)3159484
1-151364574-C-A not specified Uncertain significance (Jul 13, 2021)2236433
1-151364625-A-T not specified Uncertain significance (May 27, 2022)2387385
1-151364639-G-C not specified Uncertain significance (Aug 12, 2021)2243121
1-151364678-A-G SELENBP1-related condition Likely benign (Jul 24, 2019)3049444
1-151364930-T-G not specified Uncertain significance (Mar 23, 2022)2279568
1-151364973-C-T SELENBP1-related condition Likely benign (May 03, 2019)3037147
1-151364974-G-A SELENBP1-related condition Benign (May 15, 2019)3037494
1-151364974-G-T not specified Uncertain significance (Jan 30, 2024)3159483
1-151365196-A-G not specified Uncertain significance (Aug 31, 2023)2620894
1-151365214-G-C SELENBP1-related condition Likely benign (Jun 02, 2023)3045077
1-151365215-A-G not specified Uncertain significance (Jul 06, 2022)2355340
1-151365227-C-T Benign (Feb 27, 2018)775140
1-151365272-C-G not specified Uncertain significance (Aug 14, 2023)2618218
1-151365557-C-G SELENBP1-related condition Likely benign (Nov 23, 2020)3031521
1-151365568-C-A Extra oral halitosis • Extraoral halitosis due to methanethiol oxidase deficiency Likely pathogenic (Apr 16, 2018)549495
1-151365570-G-C not specified Uncertain significance (Aug 17, 2022)2307997
1-151365579-G-A not specified Uncertain significance (Dec 11, 2023)3159482
1-151365622-G-A Extra oral halitosis • Extraoral halitosis due to methanethiol oxidase deficiency Likely pathogenic (Apr 16, 2018)549497
1-151365626-C-G not specified Uncertain significance (May 03, 2023)2542111
1-151365637-A-G not specified Uncertain significance (Jul 13, 2021)2236434
1-151365639-T-C not specified Uncertain significance (Sep 27, 2022)2231538
1-151365649-G-A not specified Uncertain significance (Oct 31, 2022)2395988
1-151365673-C-T not specified Uncertain significance (Dec 27, 2023)3159496
1-151365797-A-C not specified Uncertain significance (Feb 15, 2023)2484033

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SELENBP1protein_codingprotein_codingENST00000368868 128432
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.23e-160.01921257000471257470.000187
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4492622830.9250.00001643048
Missense in Polyphen98105.310.930571103
Synonymous-0.2231191161.030.00000719935
Loss of Function0.3542527.00.9260.00000140285

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001070.00107
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.000.00
European (Non-Finnish)0.0001690.000167
Middle Eastern0.0001630.000163
South Asian0.0001310.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the oxidation of methanethiol, an organosulfur compound known to be produced in substantial amounts by gut bacteria (PubMed:29255262). Selenium-binding protein which may be involved in the sensing of reactive xenobiotics in the cytoplasm. May be involved in intra-Golgi protein transport (By similarity). {ECO:0000250|UniProtKB:Q8VIF7, ECO:0000269|PubMed:29255262}.;
Disease
DISEASE: Note=SELENBP1 mutations are responsible for 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. {ECO:0000269|PubMed:29255262}.;
Pathway
Selenium Metabolism and Selenoproteins;IL1 and megakaryocytes in obesity (Consensus)

Intolerance Scores

loftool
0.285
rvis_EVS
-0.64
rvis_percentile_EVS
16.53

Haploinsufficiency Scores

pHI
0.257
hipred
N
hipred_score
0.288
ghis
0.565

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.875

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Selenbp1
Phenotype
hematopoietic system phenotype; reproductive system phenotype; liver/biliary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
protein transport;oxidation-reduction process
Cellular component
fibrillar center;extracellular space;nucleolus;cytosol;membrane;extracellular exosome
Molecular function
protein binding;selenium binding;methanethiol oxidase activity