CYP46A1

cytochrome P450 family 46 subfamily A member 1, the group of Cytochrome P450 family 46

Basic information

Region (hg38): 14:99684298-99727301

Previous symbols: [ "CYP46" ]

Links

ENSG00000036530

∙ NCBI:10858 ∙ OMIM:604087 ∙ HGNC:2641 ∙ Uniprot:Q9Y6A2 ∙ 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 CYP46A1 gene.

not_specified (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP46A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006668.2. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			25 clinvar	3 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	26	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP46A1	protein_coding	protein_coding	ENST00000261835	15	42998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0145	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	156	301	0.519	0.0000189	3233
Missense in Polyphen		29	106.89	0.2713		1094
Synonymous	-0.733	134	124	1.08	0.00000791	1015
Loss of Function	4.19	3	26.1	0.115	0.00000111	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in the turnover of cholesterol. It converts cholesterol into 24S-hydroxycholesterol and, to a lesser extent, 25-hydroxycholesterol. Has also activity with xenobiotic compounds, such as clotrimazole. {ECO:0000269|PubMed:18621681, ECO:0000269|PubMed:20667828}.;
Pathway: Primary bile acid biosynthesis - Homo sapiens (human);27-Hydroxylase Deficiency;Bile Acid Biosynthesis;Congenital Bile Acid Synthesis Defect Type II;Cerebrotendinous Xanthomatosis (CTX);Zellweger Syndrome;Familial Hypercholanemia (FHCA);Congenital Bile Acid Synthesis Defect Type III;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;Endogenous sterols;Cytochrome P450 - arranged by substrate type;Biological oxidations;Metabolism;Synthesis of bile acids and bile salts via 24-hydroxycholesterol;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Metabolism of steroids (Consensus)

Recessive Scores

pRec: 0.351

Intolerance Scores

loftool: 0.259
rvis_EVS: -0.32
rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

pHI: 0.157
hipred: Y
hipred_score: 0.745
ghis: 0.505

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cyp46a1
Phenotype: homeostasis/metabolism phenotype;

Gene ontology

Biological process: bile acid biosynthetic process;cholesterol catabolic process;xenobiotic metabolic process;nervous system development;sterol metabolic process;oxidation-reduction process
Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;organelle membrane
Molecular function: iron ion binding;steroid hydroxylase activity;heme binding;cholesterol 24-hydroxylase activity