SELENBP1

selenium binding protein 1

Basic information

Region (hg38): 1:151364303-151372707

Links

ENSG00000143416 ∙ NCBI:8991 ∙ OMIM:604188 ∙ HGNC:10719 ∙ Uniprot:Q13228 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Extraoral halitosis due to methanethiol oxidase deficiency	AR	General	The clinical relevance is unclear	Biochemical	29255262

ClinVar

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

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				3	3	6
missense		2	39	1	2	44
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				1	2	3
Total	0	3	39	5	7

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)
1-151364574-C-A		not specified	Uncertain significance (Jul 13, 2021)
1-151364625-A-T		not specified	Uncertain significance (May 27, 2022)
1-151364639-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-151364678-A-G		SELENBP1-related disorder	Likely benign (Jul 24, 2019)
1-151364930-T-G		not specified	Uncertain significance (Mar 23, 2022)
1-151364973-C-T		SELENBP1-related disorder	Likely benign (May 03, 2019)
1-151364974-G-A		SELENBP1-related disorder	Benign (May 15, 2019)
1-151364974-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-151365196-A-G		not specified	Uncertain significance (Aug 31, 2023)
1-151365214-G-C		SELENBP1-related disorder	Likely benign (Jun 02, 2023)
1-151365215-A-G		not specified	Uncertain significance (Jul 06, 2022)
1-151365227-C-T			Benign (Feb 27, 2018)
1-151365272-C-G		not specified	Uncertain significance (Aug 14, 2023)
1-151365557-C-G		SELENBP1-related disorder	Likely benign (Nov 23, 2020)
1-151365568-C-A		Extra oral halitosis • Extraoral halitosis due to methanethiol oxidase deficiency	Likely pathogenic (Apr 16, 2018)
1-151365570-G-C		not specified	Uncertain significance (Aug 17, 2022)
1-151365579-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-151365622-G-A		Extra oral halitosis • Extraoral halitosis due to methanethiol oxidase deficiency	Likely pathogenic (Apr 16, 2018)
1-151365626-C-G		not specified	Uncertain significance (May 03, 2023)
1-151365637-A-G		not specified	Uncertain significance (Jul 13, 2021)
1-151365639-T-C		not specified	Uncertain significance (Sep 27, 2022)
1-151365649-G-A		not specified	Uncertain significance (Oct 31, 2022)
1-151365673-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-151365797-A-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELENBP1	protein_coding	protein_coding	ENST00000368868	12	8432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.23e-16	0.0192	125700	0	47	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.449	262	283	0.925	0.0000164	3048
Missense in Polyphen		98	105.31	0.93057		1103
Synonymous	-0.223	119	116	1.03	0.00000719	935
Loss of Function	0.354	25	27.0	0.926	0.00000140	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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