CYP4X1

cytochrome P450 family 4 subfamily X member 1, the group of Cytochrome P450 family 4

Basic information

Region (hg38): 1:47023669-47050751

Links

ENSG00000186377 ∙ NCBI:260293 ∙ OMIM:614999 ∙ HGNC:20244 ∙ Uniprot:Q8N118 ∙ 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 CYP4X1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4X1 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						0
missense			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	0

Variants in CYP4X1

This is a list of pathogenic ClinVar variants found in the CYP4X1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-47023849-C-T		not specified	Uncertain significance (Mar 28, 2024)
1-47023878-T-A		not specified	Uncertain significance (Nov 22, 2022)
1-47023882-T-A		not specified	Uncertain significance (Jun 22, 2023)
1-47023887-C-G		not specified	Uncertain significance (Mar 22, 2023)
1-47023939-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-47023972-A-T		not specified	Uncertain significance (Dec 17, 2023)
1-47023991-G-C		not specified	Uncertain significance (Aug 05, 2023)
1-47030008-A-G		not specified	Uncertain significance (May 09, 2023)
1-47030041-C-G		not specified	Uncertain significance (Dec 09, 2023)
1-47030108-C-G		not specified	Uncertain significance (Apr 09, 2024)
1-47030116-C-T		not specified	Likely benign (Oct 29, 2021)
1-47033313-T-G		not specified	Uncertain significance (Sep 15, 2021)
1-47033336-G-A		not specified	Uncertain significance (Jul 21, 2022)
1-47035833-C-G		not specified	Uncertain significance (Nov 10, 2022)
1-47036054-A-T		not specified	Uncertain significance (Jan 19, 2024)
1-47036056-C-G		not specified	Uncertain significance (Jun 03, 2024)
1-47036072-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-47036109-T-C		not specified	Uncertain significance (Nov 06, 2023)
1-47036132-C-T		not specified	Uncertain significance (May 06, 2024)
1-47036141-A-G		not specified	Likely benign (Dec 18, 2023)
1-47038678-G-T		not specified	Uncertain significance (Jan 24, 2024)
1-47038716-A-C		not specified	Uncertain significance (Oct 04, 2022)
1-47038720-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-47038726-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-47038729-A-G		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP4X1	protein_coding	protein_coding	ENST00000371901	12	89388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-12	0.337	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	220	281	0.784	0.0000139	3365
Missense in Polyphen		77	95.523	0.80609		1247
Synonymous	0.283	103	107	0.965	0.00000550	948
Loss of Function	1.12	21	27.3	0.769	0.00000133	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00238	0.00235
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000218	0.000217
South Asian	0.000851	0.000850
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Serotonergic synapse - Homo sapiens (human);nicotine degradation III;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;bupropion degradation;acetone degradation I (to methylglyoxal);Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;superpathway of tryptophan utilization;melatonin degradation I;superpathway of melatonin degradation;Arachidonic acid metabolism;nicotine degradation IV (Consensus)

Intolerance Scores

• loftool: 0.896
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.0418
• hipred: N
• hipred_score: 0.139
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp4x1

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;organelle membrane
• Molecular function: iron ion binding;heme binding;aromatase activity