CYP4F22

cytochrome P450 family 4 subfamily F member 22, the group of Cytochrome P450 family 4

Basic information

Region (hg38): 19:15508524-15552317

Links

ENSG00000171954 ∙ NCBI:126410 ∙ OMIM:611495 ∙ HGNC:26820 ∙ Uniprot:Q6NT55 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive congenital ichthyosis 5 (Strong), mode of inheritance: AR
• autosomal recessive congenital ichthyosis 5 (Strong), mode of inheritance: AR
• autosomal recessive congenital ichthyosis 5 (Strong), mode of inheritance: AR
• lamellar ichthyosis (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ichthyosis, congenital, autosomal recessive 5	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	16436457

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP4F22 gene.

• not provided (114 variants)
• Autosomal recessive congenital ichthyosis 5 (93 variants)
• Inborn genetic diseases (16 variants)
• not specified (8 variants)
• Lamellar ichthyosis (6 variants)
• Congenital ichthyosiform erythroderma (3 variants)
• Ichthyosis;Atopic eczema (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4F22 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	13	3	17
missense	2	10	49	9	3	73
nonsense	4		1			5
start loss						0
frameshift	2	2	1			5
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)	1	1	1			3
splice region			3		2	5
non coding		1	18	3	43	65
Total	9	15	72	25	49

Highest pathogenic variant AF is 0.0000920

Variants in CYP4F22

This is a list of pathogenic ClinVar variants found in the CYP4F22 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15508569-G-A		Autosomal recessive congenital ichthyosis 5	Uncertain significance (Jan 13, 2018)
19-15525307-A-G			Benign (Jun 19, 2021)
19-15525335-G-A		Autosomal recessive congenital ichthyosis 5 • not specified	Uncertain significance (Apr 17, 2023)
19-15525356-G-A		not specified • Autosomal recessive congenital ichthyosis 5	Conflicting classifications of pathogenicity (Jan 01, 2023)
19-15525386-C-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
19-15525387-G-A		Autosomal recessive congenital ichthyosis 5	Benign/Likely benign (Oct 03, 2023)
19-15525394-C-CG		Autosomal recessive congenital ichthyosis 5	Pathogenic (Aug 20, 2022)
19-15525397-A-ATAT			Uncertain significance (Jul 27, 2022)
19-15525402-C-T			Likely benign (Jun 08, 2017)
19-15525404-C-T			Likely benign (Dec 07, 2019)
19-15525412-A-G		Inborn genetic diseases	Likely benign (May 23, 2023)
19-15525425-T-C		Autosomal recessive congenital ichthyosis 5	Uncertain significance (Jan 13, 2018)
19-15525432-C-A			Likely benign (Jan 12, 2018)
19-15525446-G-T			Uncertain significance (Oct 24, 2022)
19-15525468-G-A			Likely benign (Jun 28, 2018)
19-15525496-C-T		Autosomal recessive congenital ichthyosis 5 • Inborn genetic diseases • Bladder exstrophy-epispadias-cloacal extrophy complex	Conflicting classifications of pathogenicity (Jan 25, 2024)
19-15525497-G-A			Uncertain significance (May 22, 2023)
19-15525499-C-T		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
19-15525513-C-G		Autosomal recessive congenital ichthyosis 5	Pathogenic/Likely pathogenic (Mar 17, 2024)
19-15525513-C-T		Autosomal recessive congenital ichthyosis 5	Benign/Likely benign (Dec 13, 2023)
19-15525528-G-T			Likely benign (Dec 20, 2017)
19-15525530-G-A		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
19-15525573-G-A		Autosomal recessive congenital ichthyosis 5	Conflicting classifications of pathogenicity (Nov 06, 2023)
19-15525871-T-A			Benign (Nov 11, 2018)
19-15529477-G-T			Benign (Nov 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP4F22	protein_coding	protein_coding	ENST00000269703	12	43825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000529	0.993	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.402	306	326	0.937	0.0000233	3449
Missense in Polyphen		148	155.25	0.95329		1657
Synonymous	0.642	119	128	0.928	0.00000807	1068
Loss of Function	2.42	13	26.4	0.492	0.00000140	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000217	0.000217
Finnish	0.00130	0.00129
European (Non-Finnish)	0.000326	0.000325
Middle Eastern	0.000217	0.000217
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Ichthyosis, congenital, autosomal recessive 5 (ARCI5) [MIM:604777]: A form of autosomal recessive congenital ichthyosis, a disorder of keratinization with abnormal differentiation and desquamation of the epidermis, resulting in abnormal skin scaling over the whole body. The main skin phenotypes are lamellar ichthyosis (LI) and non-bullous congenital ichthyosiform erythroderma (NCIE), although phenotypic overlap within the same patient or among patients from the same family can occur. Lamellar ichthyosis is a condition often associated with an embedment in a collodion-like membrane at birth; skin scales later develop, covering the entire body surface. Non-bullous congenital ichthyosiform erythroderma characterized by fine whitish scaling on an erythrodermal background; larger brownish scales are present on the buttocks, neck and legs. {ECO:0000269|PubMed:16436457}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Fatty acids;Eicosanoids;Miscellaneous substrates;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;Putative anti-Inflammatory metabolites formation from EPA;Vitamin E metabolism;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.470
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.2

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.283
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp4f39

Gene ontology

• Biological process: icosanoid metabolic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;organelle membrane
• Molecular function: monooxygenase activity;iron ion binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;heme binding