GeneBe

SMOX

spermine oxidase

Basic information

Region (hg38): 20:4120980-4187747

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.

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
clinvar
 3
missense
15
clinvar
1
clinvar
 16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 1 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
20-4175114-G-A not specified Uncertain significance (Apr 23, 2024)3321009
20-4175117-G-C not specified Uncertain significance (Jan 31, 2023)2467312
20-4175243-G-A not specified Uncertain significance (Mar 04, 2024)3166634
20-4177522-A-G not specified Likely benign (Oct 30, 2023)3166635
20-4177528-G-A not specified Uncertain significance (Jan 08, 2024)3166636
20-4177560-A-G not specified Uncertain significance (Nov 13, 2023)3166637
20-4181830-C-T not specified Uncertain significance (Dec 22, 2023)3166638
20-4181836-G-A not specified Uncertain significance (Sep 01, 2021)2248608
20-4181935-A-G not specified Uncertain significance (Jul 09, 2021)2235616
20-4182190-G-T Benign (Mar 29, 2018)782665
20-4182219-C-T not specified Uncertain significance (Jul 09, 2021)2377470
20-4182332-G-A not specified Uncertain significance (May 28, 2023)2521697
20-4182332-G-C not specified Uncertain significance (Apr 16, 2024)3321010
20-4182372-A-T not specified Uncertain significance (May 25, 2022)2352772
20-4182444-T-C not specified Uncertain significance (Mar 01, 2023)2461402
20-4182549-T-C not specified Uncertain significance (Nov 09, 2023)3166631
20-4182554-C-A not specified Uncertain significance (Jan 17, 2023)2476156
20-4182555-G-A not specified Uncertain significance (Sep 17, 2021)2344836
20-4182665-A-G not specified Uncertain significance (Nov 14, 2023)3166633
20-4182727-G-T Benign (Dec 31, 2019)714118
20-4182814-C-T Benign (Dec 31, 2019)716245

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SMOXprotein_codingprotein_codingENST00000305958 666768
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.4000.6001257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.262563800.6740.00002563605
Missense in Polyphen97165.010.587851508
Synonymous0.4631511580.9530.00001171110
Loss of Function3.42522.50.2220.00000113238

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003040.000304
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00006410.0000462
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.0003690.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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