CYP27B1 (cytochrome P450 family 27 subfamily B member 1)

Gene

• Entrez ID: 1594
• Gene name: Cytochrome P450 family 27 subfamily B member 1
• Gene symbol: CYP27B1
• Synonyms: CP2B, CYP1, CYP1alpha, CYP27B, P450c1, PDDR, VDD1, VDDR, VDDRI, VDR
• Chromosome: 12
• Chromosome location: 12q14.1
• Summary: This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. The protein encode

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs28934604	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs28934605	C>T	Pathogenic	Missense variant, coding sequence variant
rs28934606	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs28934607	G>A	Pathogenic	Missense variant, coding sequence variant
rs118204007	G>C	Pathogenic	Coding sequence variant, missense variant
rs118204008	G>A	Pathogenic	Coding sequence variant, missense variant
rs118204009	C>T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs118204010	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs118204011	G>A	Pathogenic	Coding sequence variant, missense variant
rs118204012	T>C	Pathogenic	Coding sequence variant, missense variant
rs387906258	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs387906259	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs387906260	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs555068245	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs568165874	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs759208930	C>T	Pathogenic	Missense variant, coding sequence variant
rs761780097	C>G,T	Pathogenic	Splice donor variant
rs763437121	C>-,CC	Pathogenic	Coding sequence variant, frameshift variant
rs767480544	G>A	Pathogenic	Coding sequence variant, missense variant
rs770204470	C>T	Pathogenic	Splice donor variant
rs780950819	->GGGTGGG	Pathogenic	Frameshift variant, coding sequence variant
rs1057520815	C>T	Pathogenic	Missense variant, coding sequence variant
rs1555202494	C>T	Likely-pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT029947	hsa-miR-26b-5p	Microarray	19088304
MIRT051080	hsa-miR-16-5p	CLASH	23622248
MIRT049861	hsa-miR-31-5p	CLASH	23622248
MIRT711962	hsa-miR-1178-5p	HITS-CLIP	19536157
MIRT711961	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT711960	hsa-miR-5681a	HITS-CLIP	19536157
MIRT711959	hsa-miR-4290	HITS-CLIP	19536157
MIRT711958	hsa-miR-6882-3p	HITS-CLIP	19536157
MIRT711957	hsa-miR-1292-5p	HITS-CLIP	19536157
MIRT711956	hsa-miR-4471	HITS-CLIP	19536157
MIRT711955	hsa-miR-8059	HITS-CLIP	19536157
MIRT711954	hsa-miR-6894-3p	HITS-CLIP	19536157
MIRT711962	hsa-miR-1178-5p	HITS-CLIP	19536157
MIRT711961	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT711960	hsa-miR-5681a	HITS-CLIP	19536157
MIRT711959	hsa-miR-4290	HITS-CLIP	19536157
MIRT711958	hsa-miR-6882-3p	HITS-CLIP	19536157
MIRT711957	hsa-miR-1292-5p	HITS-CLIP	19536157
MIRT711956	hsa-miR-4471	HITS-CLIP	19536157
MIRT711955	hsa-miR-8059	HITS-CLIP	19536157
MIRT711954	hsa-miR-6894-3p	HITS-CLIP	19536157
MIRT711962	hsa-miR-1178-5p	HITS-CLIP	19536157
MIRT711961	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT711960	hsa-miR-5681a	HITS-CLIP	19536157
MIRT711959	hsa-miR-4290	HITS-CLIP	19536157
MIRT711958	hsa-miR-6882-3p	HITS-CLIP	19536157
MIRT711957	hsa-miR-1292-5p	HITS-CLIP	19536157
MIRT711956	hsa-miR-4471	HITS-CLIP	19536157
MIRT711955	hsa-miR-8059	HITS-CLIP	19536157
MIRT711954	hsa-miR-6894-3p	HITS-CLIP	19536157
MIRT711962	hsa-miR-1178-5p	HITS-CLIP	19536157
MIRT711961	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT711960	hsa-miR-5681a	HITS-CLIP	19536157
MIRT711959	hsa-miR-4290	HITS-CLIP	19536157
MIRT711958	hsa-miR-6882-3p	HITS-CLIP	19536157
MIRT711957	hsa-miR-1292-5p	HITS-CLIP	19536157
MIRT711956	hsa-miR-4471	HITS-CLIP	19536157
MIRT711955	hsa-miR-8059	HITS-CLIP	19536157
MIRT711954	hsa-miR-6894-3p	HITS-CLIP	19536157
MIRT921207	hsa-miR-133a	CLIP-seq
MIRT921208	hsa-miR-133b	CLIP-seq
MIRT921209	hsa-miR-146a	CLIP-seq
MIRT921210	hsa-miR-146b-5p	CLIP-seq
MIRT921211	hsa-miR-3675-5p	CLIP-seq
MIRT921212	hsa-miR-4251	CLIP-seq
MIRT921213	hsa-miR-4278	CLIP-seq
MIRT921214	hsa-miR-4324	CLIP-seq
MIRT921215	hsa-miR-486-3p	CLIP-seq
MIRT921216	hsa-miR-589	CLIP-seq
MIRT1972958	hsa-miR-1207-5p	CLIP-seq
MIRT1972959	hsa-miR-3144-3p	CLIP-seq
MIRT1972960	hsa-miR-3171	CLIP-seq
MIRT1972961	hsa-miR-3200-3p	CLIP-seq
MIRT1972962	hsa-miR-4763-3p	CLIP-seq
MIRT1972963	hsa-miR-875-5p	CLIP-seq
MIRT1972964	hsa-miR-935	CLIP-seq
MIRT2208551	hsa-miR-103a	CLIP-seq
MIRT2208552	hsa-miR-107	CLIP-seq
MIRT2208553	hsa-miR-15a	CLIP-seq
MIRT2208554	hsa-miR-15b	CLIP-seq
MIRT2208555	hsa-miR-16	CLIP-seq
MIRT2208556	hsa-miR-195	CLIP-seq
MIRT2208557	hsa-miR-424	CLIP-seq
MIRT2208558	hsa-miR-4530	CLIP-seq
MIRT2208559	hsa-miR-4662a-5p	CLIP-seq
MIRT2208560	hsa-miR-4676-5p	CLIP-seq
MIRT2208561	hsa-miR-497	CLIP-seq
MIRT2208562	hsa-miR-575	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
GFI1	Repression	15947108;17207994
NFKB1	Unknown	19928584
RELA	Unknown	19928584

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004498	Function	Calcidiol 1-monooxygenase activity	IBA	21873635
GO:0004498	Function	Calcidiol 1-monooxygenase activity	IDA	9415400, 15795327, 16549446, 17023519, 22862690
GO:0004498	Function	Calcidiol 1-monooxygenase activity	TAS
GO:0005506	Function	Iron ion binding	IEA
GO:0005737	Component	Cytoplasm	IDA	15589699, 16720713
GO:0005739	Component	Mitochondrion	IBA	21873635
GO:0005739	Component	Mitochondrion	ISS
GO:0005739	Component	Mitochondrion	TAS	9333115
GO:0005741	Component	Mitochondrial outer membrane	TAS
GO:0006766	Process	Vitamin metabolic process	TAS
GO:0006816	Process	Calcium ion transport	ISS
GO:0008285	Process	Negative regulation of cell population proliferation	IDA	16549446
GO:0010956	Process	Negative regulation of calcidiol 1-monooxygenase activity	IDA	16549446
GO:0010980	Process	Positive regulation of vitamin D 24-hydroxylase activity	IDA	16549446
GO:0020037	Function	Heme binding	IEA
GO:0030282	Process	Bone mineralization	IEP	17023519
GO:0030308	Process	Negative regulation of cell growth	IMP	12496369
GO:0030500	Process	Regulation of bone mineralization	IMP	9415400
GO:0032496	Process	Response to lipopolysaccharide	IDA	12855575
GO:0033280	Process	Response to vitamin D	IBA	21873635
GO:0033280	Process	Response to vitamin D	IDA	16549446
GO:0034341	Process	Response to interferon-gamma	IDA	9282826
GO:0036378	Process	Calcitriol biosynthetic process from calciol	IBA	21873635
GO:0036378	Process	Calcitriol biosynthetic process from calciol	IDA	9415400, 15795327, 16549446, 17023519, 22862690
GO:0042359	Process	Vitamin D metabolic process	IDA	9415400
GO:0042359	Process	Vitamin D metabolic process	TAS
GO:0042369	Process	Vitamin D catabolic process	IBA	21873635
GO:0043627	Process	Response to estrogen	IEP	15795327
GO:0045618	Process	Positive regulation of keratinocyte differentiation	IMP	12496369
GO:0046697	Process	Decidualization	IEP	16720713
GO:0055074	Process	Calcium ion homeostasis	IMP	9415400
GO:0062185	Function	Secalciferol 1-monooxygenase activity	IDA	10518789
GO:0070314	Process	G1 to G0 transition	IMP	12496369
GO:0070564	Process	Positive regulation of vitamin D receptor signaling pathway	IDA	16549446

Other IDs

• MIM: 609506
• HGNC: 2606
• e!Ensembl: ENSG00000111012

Protein

• UniProt ID: O15528
• Protein name: 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial (EC 1.14.15.18) (25-OHD-1 alpha-hydroxylase) (25-hydroxyvitamin D(3) 1-alpha-hydroxylase) (VD3 1A hydroxylase) (Calcidiol 1-monooxygenase) (Cytochrome P450 subfamily XXVIIB polypeptide 1) (Cytochrome
• Protein function: A cytochrome P450 monooxygenase involved in vitamin D metabolism and in calcium and phosphorus homeostasis. Catalyzes the rate-limiting step in the activation of vitamin D in the kidney, namely the hydroxylation of 25-hydroxyvitamin D3/calcidiol
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00067	p450	41 → 505	Cytochrome P450	Domain

• Sequence:

  MTQTLKYASRVFHRVRWAPELGASLGYREYHSARRSLADIPGPSTPSFLAELFCKGGLSR
  LHELQVQGAAHFGPVWLASFGTVRTVYVAAPALVEELLRQEGPRPERCSFSPWTEHRRCR
  QRACGLLTAEGEEWQRLRSLLAPLLLRPQAAARYAGTLNNVVCDLVRRLRRQRGRGTGPP
  ALVRDVAGEFYKFGLEGIAAVLLGSRLGCLEAQVPPDTETFIRAVGSVFVSTLLTMAMPH
  WLRHLVPGPWGRLCRDWDQMFAFAQRHVERREAEAAMRNGGQPEKDLESGAHLTHFLFRE
  ELPAQSILGNVTELLLAGVDTVSNTLSWALYELSRHPEVQTALHSEITAALSPGSSAYPS
  ATVLSQLPLLKAVVKEVLRLYPVVPGNSRVPDKDIHVGDYIIPKNTLVTLCHYATSRDPA
  QFPEPNSFRPARWLGEGPTPHPFASLPFGFGKRSCMGRRLAELELQMALAQILTHFEVQP
  EPGAAPVRPKTRTVLVPERSINLQFLDR

• Sequence length: 508

Pathways

KEGG:

Steroid biosynthesis
Metabolic pathways
Parathyroid hormone synthesis, secretion and action
Tuberculosis

Reactome:

Vitamin D (calciferol) metabolism
Vitamins
Defective CYP27B1 causes Rickets vitamin D-dependent 1A (VDDR1A)

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Hypercalcemia	Hypercalcemia	rs876657376, rs387907322, rs777676129, rs387907323, rs114368325, rs6068812, rs387907324, rs777947329, rs201304511, rs769409705, rs200095793, rs876661338, rs1554095500, rs139763321, rs774432244, rs781367354	20427501
Hyperparathyroidism	Hyperparathyroidism, Secondary	rs28942098, rs121434262, rs80356649, rs121434264, rs587776558, rs587776559, rs121909259, rs104893689, rs28936684, rs104893690, rs869320729, rs104893700, rs104893705, rs104893707, rs104893709, rs863223311, rs80356650, rs193922432, rs886041637, rs201633414, rs1057519419, rs766719790, rs1281361203, rs759393722, rs1342435095, rs1200458339, rs755916513, rs1586190048, rs1558280170
Multiple sclerosis	Multiple Sclerosis	rs104895219, rs483353022, rs483353023, rs483353028, rs483353029, rs483353024, rs483353030, rs3207617, rs483353031, rs483353032, rs483353033, rs483353034, rs483353035, rs483353036, rs483353039, rs483353038, rs61731956, rs568165874, rs767480544	19525955
Vitamin d-dependent rickets	Vitamin D-dependent rickets, type 1	rs28934604, rs28934605, rs28934606, rs387906258, rs387906259, rs387906260, rs118204007, rs761780097, rs118204008, rs118204009, rs2140397731, rs770204470, rs118204010, rs118204011, rs61495246, rs121909790, rs121909791, rs121909792, rs121909802, rs121909794, rs121909795, rs121909796, rs121909797, rs121909798, rs121909800, rs121909801, rs1592107753, rs267607169, rs111033566, rs886037890, rs568165874, rs780950819, rs1057520815, rs1057521095, rs555068245, rs763437121, rs767480544, rs749537609	10518789, 22443290, 25284246, 12050193, 21700898, 30282619, 11737215, 9486994, 9837822, 10320521, 23423976, 10566658

Unknown
Disease name	Disease term	dbSNP ID	References
Dental enamel hypoplasia	Dental Enamel Hypoplasia
Dwarfism	Dwarfism
Frontal bossing	Frontal bossing
Hypocalcemic seizures	Hypocalcemic seizures
Hypocalcemic vitamin d-dependent rickets	Hypocalcemic vitamin D-dependent rickets
Milk-alkali syndrome	Milk-Alkali Syndrome		20427501
Motor delay	Clumsiness - motor delay
Polymyositis	Polymyositis, Polymyositis, Idiopathic		20427501
Polymyositis ossificans	Polymyositis Ossificans		20427501
Rachitic rosary	Rachitic rosary
Rickets	Rickets, Adult Rickets		16494812