SMS (spermine synthase)

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Gene Gene information from NCBI Gene database.
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Entrez ID 6611
Gene name Spermine synthase
Gene symbol SMS
Synonyms (NCBI Gene)
MRSRMRXSSRSPMSYSRSSpS
Chromosome X
Chromosome location Xp22.11
Summary This gene encodes a protein belonging to the spermidine/spermin synthase family and catalyzes the production of spermine from spermidine. Pseudogenes of this gene are located on chromosomes 1, 5, 6 and X. Mutations in this gene cause an X-linked intellect
SNPs SNP information provided by dbSNP.
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SNP ID Visualize variation Clinical significance Consequence
rs121434610 G>A Pathogenic, likely-pathogenic Coding sequence variant, missense variant
rs150564614 G>A Conflicting-interpretations-of-pathogenicity, likely-benign Synonymous variant, coding sequence variant
rs267607076 T>G Pathogenic Missense variant, coding sequence variant
rs371972467 C>G,T Conflicting-interpretations-of-pathogenicity Intron variant
rs397515381 G>A Pathogenic Intron variant
miRNA miRNA information provided by mirtarbase database.
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miRTarBase ID miRNA Experiments Reference
MIRT030218 hsa-miR-26b-5p Microarray 19088304
MIRT045576 hsa-miR-149-5p CLASH 23622248
MIRT042888 hsa-miR-324-3p CLASH 23622248
MIRT038683 hsa-miR-7-1-3p CLASH 23622248
MIRT682162 hsa-miR-490-3p HITS-CLIP 23706177
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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GO ID Ontology Definition Evidence Reference
GO:0005829 Component Cytosol TAS
GO:0006555 Process Methionine metabolic process TAS 7546290
GO:0006595 Process Polyamine metabolic process IEA
GO:0006595 Process Polyamine metabolic process TAS 9299240
GO:0006596 Process Polyamine biosynthetic process IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
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MIM HGNC e!Ensembl
300105 11123 ENSG00000102172
Protein Protein information from UniProt database.
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UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P52788
Protein name Spermine synthase (SPMSY) (EC 2.5.1.22) (Spermidine aminopropyltransferase)
Protein function Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).
PDB 3C6K , 3C6M
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01564 Spermine_synth 174 → 366 Domain
PF17284 Spermine_synt_N 123 → 172 Spermidine synthase tetramerisation domain Domain
PF17950 SpmSyn_N 21 → 117 S-adenosylmethionine decarboxylase N -terminal Domain
Sequence 
MAAARHSTLDFMLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFAN
LRIYPHGLVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAI
DRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRA
IMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDV
LDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILD
LSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTV
WKKAKP
Sequence length 366
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
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KEGG Pathway Reactome Pathway
Cysteine and methionine metabolism Metabolism of polyamines
Arginine and proline metabolism  
Glutathione metabolism  
Metabolic pathways  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
24
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Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Show/Hide Causal Diseases (6)
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Intellectual disability Pathogenic rs1925241775 RCV001249470
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nonpapillary renal cell carcinoma Likely pathogenic rs1924581492, rs1924586809 RCV005911007
RCV005908881
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Smith-Magenis syndrome Likely pathogenic rs1569351529 RCV000760247
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SMS-related disorder Likely pathogenic rs397515550, rs113689961, rs1556001304 RCV004527931
RCV004544192
RCV000509103
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Syndromic X-linked intellectual disability Snyder type Likely pathogenic; Pathogenic rs2146953457, rs2519671183, rs2147517480, rs2519671108, rs397515381, rs121434610, rs267607076, rs1602220706, rs397515550, rs397515551, rs1602210346, rs1924650670, rs1924586809, rs397515553, rs1924243873
View all (1 more)		 RCV002052168
RCV003333236
RCV003153129
RCV003225648
RCV000012389
View all (11 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Show/Hide Unknown Diseases (18)
Phenotype Name Clinical Significance Source Reference Evidence Score
Acute myeloid leukemia Benign ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANXIETY DISORDERS — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, RHEUMATOID — CTD 19192274
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BIPOLAR II DISORDER — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
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IL1RAPL1 3 shared diseasesDevelopmental disability, Intellectual developmental disorder, x-linked, X-linked intellectual disability 4 shared evidence sourcesDisgenet (Developmental disability), Disgenet (Intellectual developmental disorder, x-linked), HPO (Intellectual developmental disorder, x-linked), Orphanet (X-linked intellectual disability) Related via 3 shared diseases including Developmental disability, Intellectual developmental disorder, x-linked — evidence mostly Disgenet. SRM 4 shared pathwaysCysteine and methionine metabolism, Arginine and proline metabolism, Glutathione metabolism, Metabolism of polyamines Related via 4 shared pathways including Cysteine and methionine metabolism, Arginine and proline metabolism. SLC9A7 2 shared diseasesIntellectual developmental disorder, x-linked, X-linked intellectual disability 3 shared evidence sourcesDisgenet (Intellectual developmental disorder, x-linked), HPO (Intellectual developmental disorder, x-linked), Orphanet (X-linked intellectual disability) Related via 2 shared diseases including Intellectual developmental disorder, x-linked, X-linked intellectual disability — evidence mostly Disgenet. DLG3 3 shared diseasesMood disorder, Intellectual developmental disorder, x-linked, X-linked intellectual disability 4 shared evidence sourcesDisgenet (Mood disorder), Disgenet (Intellectual developmental disorder, x-linked), HPO (Intellectual developmental disorder, x-linked), Orphanet (X-linked intellectual disability) Related via 3 shared diseases including Mood disorder, Intellectual developmental disorder, x-linked — evidence mostly Disgenet. RBMX 2 shared diseasesIntellectual developmental disorder, x-linked, X-linked intellectual disability 3 shared evidence sourcesDisgenet (Intellectual developmental disorder, x-linked), HPO (Intellectual developmental disorder, x-linked), Orphanet (X-linked intellectual disability) Related via 2 shared diseases including Intellectual developmental disorder, x-linked, X-linked intellectual disability — evidence mostly Disgenet.
Schizophrenia Linked via 2 of 5 related genesIL1RAPL1, DLG3 Autism Linked via 1 of 5 related genesIL1RAPL1 Cardiovascular disease Linked via 1 of 5 related genesIL1RAPL1 Melanoma Linked via 1 of 5 related genesIL1RAPL1 Neurotic disorder Linked via 1 of 5 related genesIL1RAPL1