CYP39A1

cytochrome P450 family 39 subfamily A member 1, the group of Cytochrome P450 family 39

Basic information

Region (hg38): 6:46549579-46652830

Links

ENSG00000146233 ∙ NCBI:51302 ∙ OMIM:605994 ∙ HGNC:17449 ∙ Uniprot:Q9NYL5 ∙ 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 CYP39A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP39A1 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		1
missense			17	4		21
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	19	5	0

Variants in CYP39A1

This is a list of pathogenic ClinVar variants found in the CYP39A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-46550416-C-T		not specified	Uncertain significance (Jan 04, 2024)
6-46550418-C-T		not specified	Uncertain significance (Oct 12, 2022)
6-46587087-A-G		not specified	Uncertain significance (Feb 26, 2024)
6-46588126-A-G		not specified	Uncertain significance (Jun 10, 2024)
6-46625421-C-T		not specified	Uncertain significance (Aug 17, 2022)
6-46625429-A-G		not specified	Uncertain significance (Oct 12, 2021)
6-46625433-C-G		not specified	Uncertain significance (Jul 06, 2021)
6-46625457-C-T		not specified	Likely benign (May 28, 2024)
6-46625474-T-A		not specified	Uncertain significance (Mar 17, 2023)
6-46625485-G-A		not specified	Likely benign (Dec 17, 2023)
6-46630968-C-A		not specified	Uncertain significance (Jan 19, 2024)
6-46630970-G-A		not specified	Uncertain significance (Dec 06, 2023)
6-46631010-T-C		not specified	Uncertain significance (May 09, 2022)
6-46636408-G-C			Likely benign (Nov 01, 2022)
6-46636438-T-C		not specified	Uncertain significance (Apr 23, 2024)
6-46637839-A-T		not specified	Uncertain significance (Nov 17, 2022)
6-46637926-A-G		not specified	Likely benign (Aug 02, 2023)
6-46637931-A-C		not specified	Likely benign (Feb 17, 2024)
6-46637944-A-C		not specified	Uncertain significance (Dec 16, 2022)
6-46637947-G-C		not specified	Uncertain significance (Dec 28, 2023)
6-46637950-T-C		not specified	Uncertain significance (Sep 27, 2021)
6-46639581-T-C		not specified	Uncertain significance (Apr 19, 2024)
6-46639644-A-G		not specified	Uncertain significance (Apr 15, 2024)
6-46639654-T-C		not specified	Uncertain significance (Apr 13, 2022)
6-46642175-C-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP39A1	protein_coding	protein_coding	ENST00000275016	12	102983

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.87e-16	0.0111	125612	0	136	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0649	235	232	1.01	0.0000106	3077
Missense in Polyphen		61	66.85	0.9125		893
Synonymous	-0.941	95	84.0	1.13	0.00000405	849
Loss of Function	0.0977	24	24.5	0.979	0.00000112	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000275
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000436	0.000435
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000294	0.000290
Middle Eastern	0.000436	0.000435
South Asian	0.00262	0.00258
Other	0.00101	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the bile acid metabolism. Has a preference for 24-hydroxycholesterol, and converts it into a 7-alpha- hydroxylated product. {ECO:0000269|PubMed:10748047}.
• 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: 0.147

Intolerance Scores

• loftool: 0.428
• rvis_EVS: 2.18
• rvis_percentile_EVS: 98.07

Haploinsufficiency Scores

• pHI: 0.285
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00228

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp39a1

Gene ontology

• Biological process: bile acid biosynthetic process;cholesterol catabolic process;digestion;sterol metabolic process;bile acid catabolic process;cholesterol homeostasis;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: iron ion binding;steroid 7-alpha-hydroxylase activity;oxysterol 7-alpha-hydroxylase activity;heme binding