CYP51A1

cytochrome P450 family 51 subfamily A member 1, the group of Cytochrome P450 family 51

Basic information

Region (hg38): 7:92084987-92134803

Previous symbols: [ "CYP51" ]

Links

ENSG00000001630 ∙ NCBI:1595 ∙ OMIM:601637 ∙ HGNC:2649 ∙ Uniprot:Q16850 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract (Definitive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP51A1 gene.

• not_provided (50 variants)
• not_specified (37 variants)
• CYP51A1-related_disorder (6 variants)
• Developmental_cataract (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP51A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000786.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense		1	56	4	1	62
nonsense						0
start loss						0
frameshift			3			3
splice donor/acceptor (+/-2bp)			1			1
Total	0	1	60	9	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP51A1	protein_coding	protein_coding	ENST00000003100	10	30802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-7	0.842	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.788	239	276	0.866	0.0000139	3330
Missense in Polyphen		54	91.267	0.59167		1183
Synonymous	-0.0764	95	94.1	1.01	0.00000424	989
Loss of Function	1.52	14	21.7	0.647	9.12e-7	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00131	0.00131
Ashkenazi Jewish	0.00	0.00
East Asian	0.000602	0.000598
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.000602	0.000598
South Asian	0.000333	0.000327
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes C14-demethylation of lanosterol; it transforms lanosterol into 4,4'-dimethyl cholesta-8,14,24-triene-3-beta-ol. {ECO:0000269|PubMed:20149798, ECO:0000269|PubMed:8619637}.
• Pathway: Steroid biosynthesis - Homo sapiens (human);Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;Cholesterol Biosynthesis;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Activation of gene expression by SREBF (SREBP);Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;zymosterol biosynthesis;Endogenous sterols;Regulation of cholesterol biosynthesis by SREBP (SREBF);Cytochrome P450 - arranged by substrate type;Biological oxidations;Metabolism;cholesterol biosynthesis III (via desmosterol);cholesterol biosynthesis II (via 24,25-dihydrolanosterol);superpathway of cholesterol biosynthesis;Metabolism of steroids;cholesterol biosynthesis I;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP) (Consensus)

Intolerance Scores

• loftool: 0.390
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.340
• hipred: N
• hipred_score: 0.442
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cyp51
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; limbs/digits/tail phenotype; digestive/alimentary phenotype; muscle phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Gene ontology

• Biological process: steroid biosynthetic process;cholesterol biosynthetic process;sterol metabolic process;sterol biosynthetic process;cholesterol biosynthetic process via 24,25-dihydrolanosterol;regulation of cholesterol biosynthetic process;oxidation-reduction process;demethylation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;organelle membrane
• Molecular function: iron ion binding;sterol 14-demethylase activity;heme binding