CYP51A1

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

Basic information

Region (hg38): 7:92084986-92134803

Previous symbols: [ "CYP51" ]

Links

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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Long QT syndrome (396 variants)
• Cardiovascular phenotype (326 variants)
• not provided (142 variants)
• Long QT syndrome 11 (73 variants)
• not specified (44 variants)
• Congenital long QT syndrome (37 variants)
• Inborn genetic diseases (24 variants)
• AKAP9-related condition (5 variants)
• Long QT syndrome 1 (3 variants)
• Hypertrophic cardiomyopathy (3 variants)
• Cardiomyopathy (2 variants)
• Cardiac arrest (2 variants)
• Wolff-Parkinson-White pattern (2 variants)
• Primary dilated cardiomyopathy;Amyloidosis (1 variants)
• Arrhythmogenic right ventricular cardiomyopathy (1 variants)
• Ventricular fibrillation;Cardiomyopathy (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	2	2	5
missense			21	4	1	26
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			361	217	38	616
Total	0	0	385	223	41

Variants in CYP51A1

This is a list of pathogenic ClinVar variants found in the CYP51A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-92085476-CT-C		Long QT syndrome	Likely benign (Oct 30, 2021)
7-92085480-G-A		Long QT syndrome	Likely benign (Mar 26, 2023)
7-92085492-C-T		Long QT syndrome • Cardiovascular phenotype	Uncertain significance (Nov 15, 2022)
7-92085494-G-A		Cardiovascular phenotype	Uncertain significance (Nov 15, 2021)
7-92085497-A-T		Cardiovascular phenotype	Likely benign (Aug 16, 2022)
7-92085505-G-A		Long QT syndrome	Uncertain significance (Mar 31, 2020)
7-92085508-C-T		Long QT syndrome	Uncertain significance (Jan 25, 2024)
7-92085512-C-T		not specified	Likely benign (Mar 13, 2021)
7-92085514-A-C		Long QT syndrome	Uncertain significance (Sep 17, 2023)
7-92085534-C-T		Long QT syndrome • Cardiovascular phenotype	Uncertain significance (Oct 01, 2023)
7-92085552-C-T		Cardiovascular phenotype	Uncertain significance (Apr 29, 2022)
7-92085554-C-G		Long QT syndrome	Likely benign (Nov 27, 2023)
7-92085556-A-G		Long QT syndrome • Cardiovascular phenotype • AKAP9-related disorder	Conflicting classifications of pathogenicity (Jan 27, 2024)
7-92085570-G-A		Cardiovascular phenotype	Uncertain significance (Jan 05, 2021)
7-92085574-A-G		not specified	Likely benign (Oct 24, 2011)
7-92085581-T-G		Cardiovascular phenotype	Uncertain significance (May 15, 2023)
7-92085587-G-C		Long QT syndrome	Uncertain significance (May 22, 2023)
7-92085588-G-A		Cardiovascular phenotype	Likely benign (Jul 18, 2021)
7-92085589-T-C		Cardiovascular phenotype	Uncertain significance (Jun 24, 2022)
7-92085591-T-G		Long QT syndrome	Uncertain significance (Jan 04, 2024)
7-92085597-C-T		not specified • Congenital long QT syndrome • Cardiovascular phenotype • Long QT syndrome • Long QT syndrome 11	Benign/Likely benign (Feb 01, 2024)
7-92085611-G-C		Long QT syndrome	Uncertain significance (Jun 20, 2022)
7-92085619-C-T		Long QT syndrome • Cardiovascular phenotype	Uncertain significance (Nov 14, 2023)
7-92085620-T-C		Long QT syndrome	Likely benign (Jan 04, 2024)
7-92085623-C-T		Long QT syndrome	Likely benign (Feb 21, 2023)

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