SMOX

spermine oxidase

Basic information

Region (hg38): 20:4120979-4187747

Previous symbols: [ "C20orf16" ]

Links

ENSG00000088826 ∙ NCBI:54498 ∙ OMIM:615854 ∙ HGNC:15862 ∙ Uniprot:Q9NWM0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (9 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMOX 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
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	3

Variants in SMOX

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

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

Position	Type	Phenotype	Significance	ClinVar
20-4175117-G-C		not specified	Uncertain significance (Jan 31, 2023)
20-4175243-G-A		not specified	Uncertain significance (Mar 04, 2024)
20-4177522-A-G		not specified	Likely benign (Oct 30, 2023)
20-4177528-G-A		not specified	Uncertain significance (Jan 08, 2024)
20-4177560-A-G		not specified	Uncertain significance (Nov 13, 2023)
20-4181830-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-4181836-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-4181935-A-G		not specified	Uncertain significance (Jul 09, 2021)
20-4182190-G-T			Benign (Mar 29, 2018)
20-4182219-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-4182332-G-A		not specified	Uncertain significance (May 28, 2023)
20-4182372-A-T		not specified	Uncertain significance (May 25, 2022)
20-4182444-T-C		not specified	Uncertain significance (Mar 01, 2023)
20-4182549-T-C		not specified	Uncertain significance (Nov 09, 2023)
20-4182554-C-A		not specified	Uncertain significance (Jan 17, 2023)
20-4182555-G-A		not specified	Uncertain significance (Sep 17, 2021)
20-4182665-A-G		not specified	Uncertain significance (Nov 14, 2023)
20-4182727-G-T			Benign (Dec 31, 2019)
20-4182814-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMOX	protein_coding	protein_coding	ENST00000305958	6	66768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.400	0.600	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	256	380	0.674	0.0000256	3605
Missense in Polyphen		97	165.01	0.58785		1508
Synonymous	0.463	151	158	0.953	0.0000117	1110
Loss of Function	3.42	5	22.5	0.222	0.00000113	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000641	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000369	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Flavoenzyme which catalyzes the oxidation of spermine to spermidine. Can also use N(1)-acetylspermine and spermidine as substrates, with different affinity depending on the isoform (isozyme) and on the experimental conditions. Plays an important role in the regulation of polyamine intracellular concentration and has the potential to act as a determinant of cellular sensitivity to the antitumor polyamine analogs. May contribute to beta-alanine production via aldehyde dehydrogenase conversion of 3-amino-propanal.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);PAOs oxidise polyamines to amines;Amine Oxidase reactions;Phase I - Functionalization of compounds;Interconversion of polyamines;Metabolism of polyamines;Metabolism of amino acids and derivatives;Biological oxidations;Metabolism;spermine and spermidine degradation I (Consensus)

Recessive Scores

• pRec: 0.412

Intolerance Scores

• loftool: 0.0276
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.23

Haploinsufficiency Scores

• pHI: 0.622
• hipred: Y
• hipred_score: 0.728
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.228

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smox
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: smox
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: polyamine biosynthetic process;polyamine catabolic process;spermine catabolic process;oxidation-reduction process
• Cellular component: nucleoplasm;cytosol;nuclear membrane;intracellular membrane-bounded organelle
• Molecular function: oxidoreductase activity;polyamine oxidase activity;norspermine:oxygen oxidoreductase activity;N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity;spermine:oxygen oxidoreductase (spermidine-forming) activity