Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10682
Gene name	EBP cholestenol delta-isomerase
Gene symbol	EBP
Synonyms (NCBI Gene)	CDPX2CHO2CPXCPXDMEND
Chromosome	X
Chromosome location	Xp11.23
Summary	The protein encoded by this gene is an integral membrane protein of the endoplasmic reticulum. It is a high affinity binding protein for the antiischemic phenylalkylamine Ca2+ antagonist [3H]emopamil and the photoaffinity label [3H]azidopamil. It is simil

Show/Hide all (47)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28935174	G>A	Pathogenic	Coding sequence variant, missense variant
rs104894792	G>A	Pathogenic	Coding sequence variant, stop gained
rs104894793	C>T	Pathogenic	Coding sequence variant, stop gained
rs104894794	G>A	Pathogenic	Coding sequence variant, stop gained
rs104894795	T>C	Pathogenic	Coding sequence variant, missense variant
rs104894798	G>A	Pathogenic	Coding sequence variant, stop gained
rs104894799	C>T	Pathogenic	Coding sequence variant, stop gained
rs104894800	G>A	Pathogenic	Coding sequence variant, missense variant
rs141925556	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Coding sequence variant, missense variant
rs145509273	C>G,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant
rs587783599	G>T	Pathogenic	Missense variant, coding sequence variant
rs587783600	G>A	Pathogenic	Stop gained, coding sequence variant
rs587783601	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs587783602	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs587783603	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs587783604	TCTCA>-	Pathogenic	Frameshift variant, coding sequence variant
rs587783605	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs587783606	T>A	Pathogenic	Splice donor variant
rs587783607	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs587783608	A>C,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs587783609	T>C	Pathogenic	Missense variant, coding sequence variant
rs587783610	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs587783611	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs587783612	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs587783613	C>T	Pathogenic	Stop gained, coding sequence variant
rs587783614	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs587783615	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs587783616	T>G	Pathogenic	Stop gained, coding sequence variant
rs587783617	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs587783618	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs587783619	T>G	Likely-pathogenic	Missense variant, coding sequence variant
rs797045153	T>A	Pathogenic	Missense variant, coding sequence variant
rs797045542	->CTG	Likely-pathogenic	Inframe insertion, coding sequence variant
rs797045543	->T	Pathogenic	Frameshift variant, coding sequence variant
rs797045544	->GATA	Pathogenic	Stop gained, coding sequence variant
rs797045545	CATCACAGCTT>AG	Likely-pathogenic	Inframe indel, coding sequence variant
rs797045546	CCGCC>T	Pathogenic	Frameshift variant, coding sequence variant
rs797045547	->G	Pathogenic	Frameshift variant, coding sequence variant
rs878854358	C>A	Pathogenic	Stop gained, coding sequence variant
rs878854359	T>C	Pathogenic	Missense variant, coding sequence variant
rs886039345	C>T	Pathogenic	Missense variant, coding sequence variant
rs1064796721	TCGTGACCACATG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1569479885	G>T	Pathogenic	Splice donor variant
rs1569479901	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1569480016	->A	Pathogenic	Coding sequence variant, stop gained
rs1602090481	G>A	Pathogenic	Coding sequence variant, missense variant
rs1602091152	AG>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (94)

miRTarBase ID	miRNA	Experiments	Reference
MIRT001061	hsa-miR-218-5p	qRT-PCRWestern blot	17998940
MIRT049085	hsa-miR-92a-3p	CLASH	23622248
MIRT042892	hsa-miR-324-3p	CLASH	23622248
MIRT040389	hsa-miR-615-3p	CLASH	23622248
MIRT951446	hsa-miR-1470	CLIP-seq
MIRT951447	hsa-miR-3684	CLIP-seq
MIRT951448	hsa-miR-376a	CLIP-seq
MIRT951449	hsa-miR-376b	CLIP-seq
MIRT951450	hsa-miR-377	CLIP-seq
MIRT951451	hsa-miR-4297	CLIP-seq
MIRT951452	hsa-miR-4300	CLIP-seq
MIRT951453	hsa-miR-4318	CLIP-seq
MIRT951454	hsa-miR-4519	CLIP-seq
MIRT951455	hsa-miR-4530	CLIP-seq
MIRT951456	hsa-miR-4646-3p	CLIP-seq
MIRT951457	hsa-miR-4648	CLIP-seq
MIRT951458	hsa-miR-4654	CLIP-seq
MIRT951459	hsa-miR-4667-3p	CLIP-seq
MIRT951460	hsa-miR-4753-3p	CLIP-seq
MIRT951461	hsa-miR-4769-5p	CLIP-seq
MIRT951462	hsa-miR-515-3p	CLIP-seq
MIRT951463	hsa-miR-519e	CLIP-seq
MIRT951464	hsa-miR-548g	CLIP-seq
MIRT951465	hsa-miR-643	CLIP-seq
MIRT951466	hsa-miR-920	CLIP-seq
MIRT951467	hsa-miR-942	CLIP-seq
MIRT1981829	hsa-miR-3938	CLIP-seq
MIRT951451	hsa-miR-4297	CLIP-seq
MIRT951453	hsa-miR-4318	CLIP-seq
MIRT951454	hsa-miR-4519	CLIP-seq
MIRT951455	hsa-miR-4530	CLIP-seq
MIRT951462	hsa-miR-515-3p	CLIP-seq
MIRT951463	hsa-miR-519e	CLIP-seq
MIRT951464	hsa-miR-548g	CLIP-seq
MIRT1981830	hsa-miR-576-5p	CLIP-seq
MIRT2216679	hsa-miR-1207-5p	CLIP-seq
MIRT2216680	hsa-miR-1248	CLIP-seq
MIRT2216681	hsa-miR-3127-3p	CLIP-seq
MIRT1981829	hsa-miR-3938	CLIP-seq
MIRT2216682	hsa-miR-4514	CLIP-seq
MIRT2216683	hsa-miR-4692	CLIP-seq
MIRT2216684	hsa-miR-4736	CLIP-seq
MIRT2216685	hsa-miR-4763-3p	CLIP-seq
MIRT2216686	hsa-miR-4763-5p	CLIP-seq
MIRT2216687	hsa-miR-550a	CLIP-seq
MIRT2216688	hsa-miR-578	CLIP-seq
MIRT2216689	hsa-miR-581	CLIP-seq
MIRT2216679	hsa-miR-1207-5p	CLIP-seq
MIRT2520635	hsa-miR-1286	CLIP-seq
MIRT951446	hsa-miR-1470	CLIP-seq
MIRT2520636	hsa-miR-2355-3p	CLIP-seq
MIRT2520637	hsa-miR-3128	CLIP-seq
MIRT2520638	hsa-miR-3182	CLIP-seq
MIRT2520639	hsa-miR-4268	CLIP-seq
MIRT2520640	hsa-miR-4275	CLIP-seq
MIRT951452	hsa-miR-4300	CLIP-seq
MIRT951453	hsa-miR-4318	CLIP-seq
MIRT2216682	hsa-miR-4514	CLIP-seq
MIRT951456	hsa-miR-4646-3p	CLIP-seq
MIRT951457	hsa-miR-4648	CLIP-seq
MIRT951458	hsa-miR-4654	CLIP-seq
MIRT951459	hsa-miR-4667-3p	CLIP-seq
MIRT2216683	hsa-miR-4692	CLIP-seq
MIRT2520641	hsa-miR-4720-5p	CLIP-seq
MIRT2216684	hsa-miR-4736	CLIP-seq
MIRT2520642	hsa-miR-4759	CLIP-seq
MIRT2216685	hsa-miR-4763-3p	CLIP-seq
MIRT951461	hsa-miR-4769-5p	CLIP-seq
MIRT2520643	hsa-miR-4799-3p	CLIP-seq
MIRT951464	hsa-miR-548g	CLIP-seq
MIRT951466	hsa-miR-920	CLIP-seq
MIRT2216679	hsa-miR-1207-5p	CLIP-seq
MIRT2520635	hsa-miR-1286	CLIP-seq
MIRT951446	hsa-miR-1470	CLIP-seq
MIRT2520636	hsa-miR-2355-3p	CLIP-seq
MIRT2520637	hsa-miR-3128	CLIP-seq
MIRT2520638	hsa-miR-3182	CLIP-seq
MIRT2520640	hsa-miR-4275	CLIP-seq
MIRT951452	hsa-miR-4300	CLIP-seq
MIRT951453	hsa-miR-4318	CLIP-seq
MIRT2216682	hsa-miR-4514	CLIP-seq
MIRT951456	hsa-miR-4646-3p	CLIP-seq
MIRT951457	hsa-miR-4648	CLIP-seq
MIRT951458	hsa-miR-4654	CLIP-seq
MIRT951459	hsa-miR-4667-3p	CLIP-seq
MIRT2216683	hsa-miR-4692	CLIP-seq
MIRT2520641	hsa-miR-4720-5p	CLIP-seq
MIRT2216684	hsa-miR-4736	CLIP-seq
MIRT2520642	hsa-miR-4759	CLIP-seq
MIRT2216685	hsa-miR-4763-3p	CLIP-seq
MIRT951461	hsa-miR-4769-5p	CLIP-seq
MIRT2520643	hsa-miR-4799-3p	CLIP-seq
MIRT951464	hsa-miR-548g	CLIP-seq
MIRT951466	hsa-miR-920	CLIP-seq

Show/Hide all (42)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000247	Function	C-8 sterol isomerase activity	IBA
GO:0000247	Function	C-8 sterol isomerase activity	IEA
GO:0000247	Function	C-8 sterol isomerase activity	ISS
GO:0004769	Function	Steroid Delta-isomerase activity	EXP	10391218, 10391219
GO:0004769	Function	Steroid Delta-isomerase activity	IBA
GO:0004769	Function	Steroid Delta-isomerase activity	IDA	9894009, 10391219
GO:0004769	Function	Steroid Delta-isomerase activity	IMP	10391219
GO:0005515	Function	Protein binding	IPI	25910212, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005635	Component	Nuclear envelope	IDA	10406945
GO:0005635	Component	Nuclear envelope	IEA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	10406945
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	10406945
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	ISM	7706302
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006694	Process	Steroid biosynthetic process	IEA
GO:0006695	Process	Cholesterol biosynthetic process	IBA
GO:0006695	Process	Cholesterol biosynthetic process	IDA	9894009
GO:0006695	Process	Cholesterol biosynthetic process	IEA
GO:0008202	Process	Steroid metabolic process	IEA
GO:0008203	Process	Cholesterol metabolic process	IEA
GO:0008203	Process	Cholesterol metabolic process	IMP	10391219
GO:0016020	Component	Membrane	IEA
GO:0016125	Process	Sterol metabolic process	IEA
GO:0016126	Process	Sterol biosynthetic process	IEA
GO:0016126	Process	Sterol biosynthetic process	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016853	Function	Isomerase activity	IEA
GO:0030097	Process	Hemopoiesis	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031965	Component	Nuclear membrane	IDA
GO:0033489	Process	Cholesterol biosynthetic process via desmosterol	TAS
GO:0033490	Process	Cholesterol biosynthetic process via lathosterol	TAS
GO:0033963	Function	Cholesterol-5,6-oxide hydrolase activity	IEA
GO:0033963	Function	Cholesterol-5,6-oxide hydrolase activity	IMP	20615952
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0043931	Process	Ossification involved in bone maturation	IMP	10391219
GO:0047750	Function	Cholestenol delta-isomerase activity	IEA

MIM	HGNC	e!Ensembl
300205	3133	ENSG00000147155

Q15125

Protein name

3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase (EC 5.3.3.5) (Cholestenol Delta-isomerase) (Cholesterol-5,6-epoxide hydrolase subunit EBP) (EC 3.3.2.11) (Delta(8)-Delta(7) sterol isomerase) (D8-D7 sterol isomerase) (Emopamil-binding protein)

Protein function

Isomerase that catalyzes the conversion of Delta(8)-sterols to their corresponding Delta(7)-isomers a catalytic step in the postlanosterol biosynthesis of cholesterol. {ECO:0000269|PubMed:12760743, ECO:0000269|PubMed:8798407, ECO:0000269|PubMed:

PDB

6OHT , 6OHU , 8W0R , 8W0S

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05241	EBP	96 → 207		Family

Sequence

MTTNAGPLHPYWPQHLRLDNFVPNDRPTWHILAGLFSVTGVLVVTTWLLSGRAAVVPLGT
WRRLSLCWFAVCGFIHLVIEGWFVLYYEDLLGDQAFLSQLWKEYAKGDSRYILGDNFTVC
METITACLWGPLSLWVVIAFLRQHPLRFILQLVVSVGQIYGDVLYFLTEHRDGFQHGELG
HPLYFWFYFVFMNALWLVLPGVLVLDAVKHLTHAQSTLDAKATKAKSKKN

Sequence length

230

Interactions

View interactions

	KEGG		Reactome
	Steroid biosynthesis Metabolic pathways		Cholesterol biosynthesis via desmosterol Cholesterol biosynthesis via lathosterol

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)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Chondrodysplasia punctata 2 X-linked dominant	Likely pathogenic; Pathogenic	rs372974717, rs1569479885, rs587783599, rs587783600, rs587783601, rs587783602, rs587783603, rs587783604, rs587783605, rs587783606, rs587783607, rs587783608, rs587783609, rs587783610, rs587783611 View all (28 more)	RCV002227567 RCV002273108 RCV000145922 RCV000145924 RCV000145925 View all (39 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CHONDRODYSPLASIA PUNCTATA 2, X-LINKED DOMINANT, ATYPICAL	Pathogenic	rs878854358	RCV000190981	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Connective tissue disorder	Likely pathogenic; Pathogenic	rs104894800	RCV002276542	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
EBP-related disorder	Likely pathogenic	rs2519522435	RCV003397765	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MEND syndrome	Pathogenic; Likely pathogenic	rs587783599, rs797045153, rs878854359, rs886039345, rs28935174, rs104894795	RCV000190980 RCV000190982 RCV000190983 RCV001824133 RCV004795393 RCV000012248 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nonpapillary renal cell carcinoma	Likely pathogenic; Pathogenic	rs587783601	RCV005888126	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Pathogenic	rs2519522184, rs104894799	RCV005930331 RCV005887448	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (17)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
Acute myeloid leukemia	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHONDRODYSPLASIA PUNCTATA	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHONDRODYSPLASIA PUNCTATA 2, X-LINKED DOMINANT	—	GWAS catalog, HPO GWAS catalog, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHONDRODYSPLASIA PUNCTATA, X-LINKED DOMINANT TYPE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cleft palate	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONNECTIVE TISSUE DISEASES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED CHONDRODYSPLASIA PUNCTATA 2	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED DOMINANT CHONDRODYSPLASIA PUNCTATA	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

EBP (EBP cholestenol delta-isomerase)