TGDS (TDP-glucose 4,6-dehydratase)

Gene

• Entrez ID: 23483
• Gene name: TDP-glucose 4,6-dehydratase
• Gene symbol: TGDS
• Synonyms (NCBI Gene): CATMANS, SDR2E1, TDPGD
• Chromosome: 13
• Chromosome location: 13q32.1
• Summary: The protein encoded by this gene is a member of the short-chain dehydrogenases/reductases (SDR) superfamily, and is thought to contain a nicotinamide adenine dinucleotide (NAD) binding domain. This large SDR family of enzymes is involved in the metabolism

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140430952	C>A,T	Pathogenic	Intron variant, missense variant, non coding transcript variant, coding sequence variant
rs544436734	A>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs724160004	T>C	Pathogenic	Intron variant, non coding transcript variant, missense variant, coding sequence variant
rs724160005	T>C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs727502808	A>C,G	Pathogenic	Intron variant, non coding transcript variant, synonymous variant, coding sequence variant, missense variant
rs727502809	CT>-	Pathogenic	Intron variant, non coding transcript variant, frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT023189	hsa-miR-124-3p	Microarray	18668037
MIRT1420993	hsa-miR-1179	CLIP-seq
MIRT1420994	hsa-miR-4272	CLIP-seq
MIRT1420995	hsa-miR-4422	CLIP-seq
MIRT1420996	hsa-miR-95	CLIP-seq
MIRT2126335	hsa-miR-579	CLIP-seq
MIRT2641096	hsa-miR-1304	CLIP-seq
MIRT2641097	hsa-miR-150	CLIP-seq
MIRT2641098	hsa-miR-1827	CLIP-seq
MIRT2641099	hsa-miR-4452	CLIP-seq
MIRT2641100	hsa-miR-4713-5p	CLIP-seq
MIRT2641101	hsa-miR-4735-5p	CLIP-seq
MIRT2641102	hsa-miR-4738-3p	CLIP-seq
MIRT2641103	hsa-miR-4789-5p	CLIP-seq
MIRT2641104	hsa-miR-532-3p	CLIP-seq
MIRT2641105	hsa-miR-544	CLIP-seq
MIRT2641106	hsa-miR-590-3p	CLIP-seq
MIRT2641096	hsa-miR-1304	CLIP-seq
MIRT2641097	hsa-miR-150	CLIP-seq
MIRT2641098	hsa-miR-1827	CLIP-seq
MIRT2641099	hsa-miR-4452	CLIP-seq
MIRT2641100	hsa-miR-4713-5p	CLIP-seq
MIRT2641102	hsa-miR-4738-3p	CLIP-seq
MIRT2641104	hsa-miR-532-3p	CLIP-seq
MIRT2641105	hsa-miR-544	CLIP-seq
MIRT2641106	hsa-miR-590-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0005515	Function	Protein binding	IPI	32814053
GO:0008460	Function	DTDP-glucose 4,6-dehydratase activity	IBA
GO:0008460	Function	DTDP-glucose 4,6-dehydratase activity	IEA
GO:0009225	Process	Nucleotide-sugar metabolic process	IEA
GO:0016829	Function	Lyase activity	IEA

Other IDs

• MIM: 616146
• HGNC: 20324
• e!Ensembl: ENSG00000088451

Protein

• UniProt ID: O95455
• Protein name: dTDP-D-glucose 4,6-dehydratase (EC 4.2.1.46)
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF16363	GDP_Man_Dehyd	21 → 327	GDP-mannose 4,6 dehydratase	Domain

• Sequence:

  MSAACWEEPWGLPGGFAKRVLVTGGAGFIASHMIVSLVEDYPNYMIINLDKLDYCASLKN
  LETISNKQNYKFIQGDICDSHFVKLLFETEKIDIVLHFAAQTHVDLSFVRAFEFTYVNVY
  GTHVLVSAAHEARVEKFIYVSTDEVYGGSLDKEFDESSPKQPTNPYASSKAAAECFVQSY
  WEQYKFPVVITRSSNVYGPHQYPEKVIPKFISLLQHNRKCCIHGSGLQTRNFLYATDVVE
  AFLTVLKKGKPGEIYNIGTNFEMSVVQLAKELIQLIKETNSESEMENWVDYVNDRPTNDM
  RYPMKSEKIHGLGWRPKVPWKEGIKKTIEWYRENFHNWKNVEKALEPFPV

• Sequence length: 350

Pathways

KEGG:

Biosynthesis of various nucleotide sugars
Metabolic pathways
Biosynthesis of nucleotide sugars

Associated diseases

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Catel-Manzke syndrome	Likely pathogenic; Pathogenic	rs1888779255, rs140430952, rs544436734, rs724160004, rs727502808, rs724160005, rs1889172738, rs775273838	RCV002810053 RCV000149817 RCV000149818 RCV000149819 RCV000149820 RCV000149822 RCV002510448 RCV002790047	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
TGDS-related disorder	Likely pathogenic; Pathogenic	rs140430952	RCV003415988	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CATEL MANZKE SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Aortic coarctation	Aortic Coarctation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Atrial Septal Defects	Atrial Septal Defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Catel Manzke syndrome	Catel Manzke Syndrome	BEFREE	25480037, 28422407, 31769200		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Catel Manzke syndrome	Catel Manzke Syndrome	GENOMICS_ENGLAND_DG	25480037		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Catel Manzke syndrome	Catel Manzke Syndrome	ORPHANET_DG	25480037		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Catel Manzke syndrome	Catel Manzke Syndrome	UNIPROT_DG	25480037		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Catel Manzke syndrome	Catel Manzke Syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Catel Manzke syndrome	Catel Manzke Syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Catel-Manzke syndrome	Catel Manzke Syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Chronic otitis media	Otitis media	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	BEFREE	31769200		★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	BEFREE	31769200		★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Camptodactyly	Congenital Camptodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital exomphalos	Congenital Exomphalos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital pectus carinatum	Congenital Pectus Carinatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital pectus excavatum	Congenital Pectus Excavatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	BEFREE	29723721, 29787954		★☆☆☆☆ Found in Text Mining only
Depressive disorder	Mental Depression	BEFREE	29560848, 29723721, 29787954		★☆☆☆☆ Found in Text Mining only
Dextrocardia	Dextrocardia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glossoptosis	Glossoptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lymphangioma, Cystic	Cystic hygroma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mental Depression	Mental Depression	BEFREE	29560848, 29723721, 29787954		★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Multiple congenital anomalies	Multiple Congenital Anomalies	CLINVAR_DG	14564220, 18501694, 21834032, 24326962, 25480037, 26366375, 28422407		★☆☆☆☆ Found in Text Mining only
Overriding aorta	Overriding aorta	HPO_DG			★☆☆☆☆ Found in Text Mining only
Presenile dementia	Senile Dementia	BEFREE	29723721, 29787954		★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Temtamy preaxial brachydactyly syndrome	Temtamy Preaxial Brachydactyly Syndrome	BEFREE	28422407		★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only