SELENBP1

Chr 1AR

selenium binding protein 1

Also known as: EHMTO, HEL-S-134P, LPSB, MTO, SBP56, SP56, hSBP

NCBI Gene: 8991 ENSG00000143416 UniProt: Q13228 OMIM: 604188

This protein catalyzes the oxidation of methanethiol, an organosulfur compound produced by gut bacteria, and functions as a selenium-binding protein involved in sensing reactive xenobiotics. Mutations cause extraoral halitosis due to methanethiol oxidase deficiency, inherited in an autosomal recessive pattern. The gene shows low constraint to loss-of-function variation, consistent with a recessive disorder affecting a specific metabolic pathway.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

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. [provided by RefSeq, Apr 2012]

OMIM ResearchGenerating clinical summary…

ARLOEUF 1.291 OMIM phenotype

Clinical Summary— SELENBP1

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Gene-Disease Validity (ClinGen)

extraoral halitosis due to methanethiol oxidase deficiency · ARModerate

Moderate evidence — consider for supplementary testing

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

4 unique Pathogenic / Likely Pathogenic· 75 VUS of 123 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.29LOEUF

pLI 0.000

Z-score 0.35

OE 0.93 (0.67–1.29)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.45Z-score

OE missense 0.92 (0.83–1.02)

262 obs / 283.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.93 (0.67–1.29)

0≤0.351.4

Missense OE?0.92 (0.83–1.02)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 25 / 27.0Missense obs/exp: 262 / 283.3Syn Z: -0.22

ClinVar Variant Classifications

123 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic3

VUS75

Likely Benign8

Benign8

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	1	2	0	0	3
VUS	0	75	0	0	75
Likely Benign	0	1	3	4	8
Benign	0	3	2	3	8
Total	2	81	5	7	95

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

15 pathogenic / likely-pathogenic (of 21) ClinVar copy-number / structural variants overlap SELENBP1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →