CleftGeneDB-Search

Gene: SC5D

Basic information

Tag	Content
Uniprot ID	O75845; O00119; Q6GTM5; Q9UK15;
Entrez ID	6309
Genbank protein ID	EAW67520.1; BAB68218.1; BAA33729.1; BAD96406.1; BAA18970.1; AAH12333.1; BAD96861.1; AAF00544.1; AAH50427.1; BAG35518.1;
Genbank nucleotide ID	NM_001024956.2; NM_006918.4;
Ensembl protein ID	ENSP00000264027; ENSP00000376539;
Ensembl nucleotide ID	ENSG00000109929
Gene name	Lathosterol oxidase
Gene symbol	SC5D
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type
Developmental stage
Data sources	Homology search
Reference
Functional description	Catalyzes a dehydrogenation to introduce C5-6 double bond into lathosterol in cholesterol biosynthesis.
Sequence	MDLVLRVADY YFFTPYVYPA TWPEDDIFRQ AISLLIVTNV GAYILYFFCA TLSYYFVFDH 60 ALMKHPQFLK NQVRREIKFT VQALPWISIL TVALFLLEIR GYSKLHDDLG EFPYGLFELV 120 VSIISFLFFT DMFIYWIHRG LHHRLVYKRL HKPHHIWKIP TPFASHAFHP IDGFLQSLPY 180 HIYPFIFPLH KVVYLSLYIL VNIWTISIHD GDFRVPQILQ PFINGSAHHT DHHMFFDYNY 240 GQYFTLWDRI GGSFKNPSSF EGKGPLSYVK EMTEGKRSSH SGNGCKNEKL FNGEFTKTE 299

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression in different tissues (GTEx V7)

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

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Relation	Gene symbol	Entrez ID	UniProt ID	Cleft type	Species	Evidence	Details
1:1 ortholog	Sc5d	235293	O88822	CPO	Mus musculus	Publication	More>>
1:1 ortholog		100520925	A0A4X1VKK3		Sus scrofa	Prediction	More>>
1:1 ortholog	SC5D	525154	Q3SYX8		Bos taurus	Prediction	More>>
1:1 ortholog	SC5D		E2R5C8		Canis lupus familiaris	Prediction	More>>
1:1 ortholog	SC5D		A0A452DVT9		Capra hircus	Prediction	More>>
1:1 ortholog	SC5D	100063543	F6PHM2		Equus caballus	Prediction	More>>
1:1 ortholog	SC5D	6309	O75845		Homo sapiens	Prediction	More>>
1:1 ortholog	SC5D	451624	A0A2J8N215		Pan troglodytes	Prediction	More>>
1:1 ortholog	Sc5d	114100	Q9EQS5		Rattus norvegicus	Prediction	More>>
1:1 ortholog	sc5d		F1QG97		Danio rerio	Prediction	More>>

Showing 1 to 10 of 10 entries

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Other genetic variants/mutations

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ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs104894295	p.Arg29Gln	missense variant	Lathosterolosis (LATHST)	NC_000011.10:g.121303461G>A	UniProt,dbSNP
rs104894297	p.Tyr46Ser	missense variant	Lathosterolosis (LATHST)	NC_000011.10:g.121303512A>C	UniProt,dbSNP
rs104894296	p.Gly211Asp	missense variant	Lathosterolosis (LATHST)	NC_000011.10:g.121307244G>A	UniProt,dbSNP
VAR_014423	p.Arg29Gln	missense variant	Lathosterolosis (LATHST)	NC_000011.10:g.121303461G>A	UniProt
VAR_020829	p.Tyr46Ser	missense variant	Lathosterolosis (LATHST)	NC_000011.10:g.121303512A>C	UniProt
VAR_014424	p.Gly211Asp	missense variant	Lathosterolosis (LATHST)	NC_000011.10:g.121307244G>A	UniProt
rs1240163598	p.Val17Met	missense variant	-	NC_000011.10:g.121303424G>A	TOPMed,gnomAD
rs927217561	p.Ser33Asn	missense variant	-	NC_000011.10:g.121303473G>A	TOPMed,gnomAD
rs762728349	p.Arg74Leu	missense variant	-	NC_000011.10:g.121304371G>T	TOPMed,gnomAD
rs762728349	p.Arg74His	missense variant	-	NC_000011.10:g.121304371G>A	TOPMed,gnomAD
rs907885684	p.Gly101Asp	missense variant	-	NC_000011.10:g.121304452G>A	TOPMed,gnomAD
rs1301468278	p.Pro113Ser	missense variant	-	NC_000011.10:g.121304487C>T	TOPMed,gnomAD
rs907365711	p.Phe133Leu	missense variant	-	NC_000011.10:g.121306441C>G	TOPMed,gnomAD
rs1160124045	p.Arg144Ile	missense variant	-	NC_000011.10:g.121306473G>T	TOPMed,gnomAD
rs775350797	p.Lys148Glu	missense variant	-	NC_000011.10:g.121306484A>G	TOPMed,gnomAD
rs1182798978	p.Ser177Asn	missense variant	-	NC_000011.10:g.121307142G>A	TOPMed,gnomAD
rs1465426900	p.Pro188Gln	missense variant	-	NC_000011.10:g.121307175C>A	TOPMed,gnomAD
rs1465426900	p.Pro188Leu	missense variant	-	NC_000011.10:g.121307175C>T	TOPMed,gnomAD
rs1237177836	p.Ile206Val	missense variant	-	NC_000011.10:g.121307228A>G	TOPMed,gnomAD
rs1250786427	p.Tyr238Cys	missense variant	-	NC_000011.10:g.121307325A>G	TOPMed,gnomAD

Showing 1 to 20 of 243 entries

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Disease or phenotype associated information

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Disease ID	Disease Name	Disease Type	Source
C0000768	Congenital Abnormality	group	BEFREE
C0003803	Arnold Chiari Malformation	disease	HPO
C0005745	Blepharoptosis	disease	HPO
C0008372	Intrahepatic Cholestasis	disease	HPO
C0008925	Cleft Palate	disease	BEFREE
C0011053	Deafness	phenotype	HPO
C0014544	Epilepsy	disease	HPO
C0015934	Fetal Growth Retardation	phenotype	HPO
C0017566	Gingival Hyperplasia	phenotype	HPO
C0017567	Gingival Hypertrophy	disease	HPO
C0018772	Hearing Loss, Partial	phenotype	HPO
C0019209	Hepatomegaly	phenotype	HPO
C0020796	Profound Mental Retardation	disease	CTD_human
C0021296	Infant, Small for Gestational Age	phenotype	HPO
C0023895	Liver diseases	group	CTD_human
C0025299	Meningocele	disease	HPO
C0025362	Mental Retardation	disease	BEFREE
C0025363	Mental Retardation, Psychosocial	disease	CTD_human
C0025990	Micrognathism	disease	BEFREE;HPO
C0026827	Muscle hypotonia	phenotype	HPO

Showing 1 to 20 of 98 entries

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

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GO ID	GO Term	Evidence
GO:0000248	C-5 sterol desaturase activity	EXP
GO:0000248	C-5 sterol desaturase activity	IBA
GO:0005506	iron ion binding	IEA
GO:0016491	oxidoreductase activity	IBA

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GO:Biological Process

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GO ID	GO Term	Evidence
GO:0006629	lipid metabolic process	TAS
GO:0016126	sterol biosynthetic process	IBA
GO:0033489	cholesterol biosynthetic process via desmosterol	TAS
GO:0033490	cholesterol biosynthetic process via lathosterol	IBA
GO:0033490	cholesterol biosynthetic process via lathosterol	TAS
GO:0045540	regulation of cholesterol biosynthetic process	TAS
GO:0055114	oxidation-reduction process	IEA

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GO:Cellular Component

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GO ID	GO Term	Evidence
GO:0005789	endoplasmic reticulum membrane	IBA
GO:0005789	endoplasmic reticulum membrane	TAS
GO:0016020	membrane	IBA
GO:0016021	integral component of membrane	IEA

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Reactome Pathway

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Reactome ID	Reactome Term	Evidence
R-HSA-1430728	Metabolism	TAS
R-HSA-1655829	Regulation of cholesterol biosynthesis by SREBP (SREBF)	TAS
R-HSA-191273	Cholesterol biosynthesis	TAS
R-HSA-2426168	Activation of gene expression by SREBF (SREBP)	TAS
R-HSA-556833	Metabolism of lipids	TAS
R-HSA-6807047	Cholesterol biosynthesis via desmosterol	TAS
R-HSA-6807062	Cholesterol biosynthesis via lathosterol	TAS
R-HSA-8957322	Metabolism of steroids	TAS

Showing 1 to 8 of 8 entries

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Drugs and compounds information

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ID	Drug Name	Action	PubMed
C000944	dicrotophos	dicrotophos results in decreased expression of SC5D mRNA	28302478
C002994	ethylene dimethanesulfonate	ethylene dimethanesulfonate results in decreased expression of SC5D mRNA	22711419
C006253	pirinixic acid	[pirinixic acid binds to and results in increased activity of PPARA protein] which results in decreased expression of SC5D mRNA	19710929
C006253	pirinixic acid	pirinixic acid results in decreased expression of SC5D mRNA	18445702; 23811191;
C006253	pirinixic acid	pirinixic acid results in increased expression of SC5D mRNA	15777286; 20059764;
C006253	pirinixic acid	PPARA protein affects the reaction [pirinixic acid results in increased expression of SC5D mRNA]	15777286
C006253	pirinixic acid	PPARA protein promotes the reaction [pirinixic acid results in increased expression of SC5D mRNA]	20059764
C006780	bisphenol A	bisphenol A results in increased expression of SC5D mRNA	21932408; 25270620;
C006780	bisphenol A	[Tetrachlorodibenzodioxin co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with Diethylhexyl Phthalate co-treated with bisphenol A] results in decreased expression of SC5D mRNA	28433925
C006780	bisphenol A	bisphenol A results in decreased expression of SC5D mRNA	25181051; 30816183;
C007738	fluoranthene	fluoranthene results in decreased expression of SC5D mRNA	28329830
C008340	mecoprop	[Herbicides co-treated with 1-aminomethylphosphonic acid co-treated with mecoprop co-treated with acetochlor co-treated with 2,4-Dichlorophenoxyacetic Acid] results in decreased expression of SC5D mRNA	20566314
C009505	4,4'-diaminodiphenylmethane	4,4'-diaminodiphenylmethane results in decreased expression of SC5D mRNA	18648102
C010974	glyphosate	glyphosate results in increased expression of SC5D mRNA	25636363
C012589	trichostatin A	trichostatin A results in increased expression of SC5D mRNA	24935251
C014024	2,4,5,2',4',5'-hexachlorobiphenyl	[Tetrachlorodibenzodioxin co-treated with 2,4,5,2',4',5'-hexachlorobiphenyl co-treated with Diethylhexyl Phthalate co-treated with bisphenol A] results in decreased expression of SC5D mRNA	28433925
C016030	pantogab	pantogab results in decreased expression of SC5D mRNA	17379144
C016104	sodium bichromate	sodium bichromate results in decreased expression of SC5D mRNA	24612858
C016403	2,4-dinitrotoluene	2,4-dinitrotoluene affects the expression of SC5D mRNA	21346803
C016527	isoquercitrin	[isoquercitrin co-treated with Hydrogen Peroxide] results in increased expression of SC5D mRNA	18032389

Showing 1 to 20 of 185 entries

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Functional annotations

Keywords

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Keyword ID	Keyword Term
KW-0225	Disease mutation
KW-0256	Endoplasmic reticulum
KW-0408	Iron
KW-0443	Lipid metabolism
KW-0444	Lipid biosynthesis
KW-0472	Membrane
KW-0560	Oxidoreductase
KW-0597	Phosphoprotein
KW-0752	Steroid biosynthesis
KW-0753	Steroid metabolism
KW-0756	Sterol biosynthesis
KW-0812	Transmembrane
KW-1133	Transmembrane helix
KW-1185	Reference proteome
KW-1207	Sterol metabolism

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Interpro

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InterPro ID	InterPro Term
IPR006694	Fatty_acid_hydroxylase

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PROSITE

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Pfam

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Pfam ID	Pfam Term
PF04116	FA_hydroxylase

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Gene: SC5D

Basic information

Gene expression information

Gene expression in different tissues (GTEx V7)

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Other genetic variants/mutations

Disease or phenotype associated information

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Drugs and compounds information

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction