GeneBe

CYP4V2

cytochrome P450 family 4 subfamily V member 2, the group of Cytochrome P450 family 4

Basic information

Region (hg38): 4:186191567-186213463

Links

ENSG00000145476 ∙ NCBI:285440 ∙ OMIM:608614 ∙ HGNC:23198 ∙ Uniprot:Q6ZWL3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Bietti crystalline corneoretinal dystrophy (Strong), mode of inheritance: AR
  • Bietti crystalline corneoretinal dystrophy (Supportive), mode of inheritance: AR
  • Bietti crystalline corneoretinal dystrophy (Strong), mode of inheritance: AR
  • Bietti crystalline corneoretinal dystrophy (Definitive), mode of inheritance: AR
  • Bietti crystalline corneoretinal dystrophy (Definitive), mode of inheritance: AR
  • Bietti crystalline corneoretinal dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Bietti crystalline corneoretinal dystrophyARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic5299874; 306693; 3493804; 2783846; 11001583; 15042513; 18398705; 19508456; 21385027; 21565171; 22087103; 22497028; 22605929; 22693542; 22772592; 23143451; 23221965; 23242590; 23538635
Subclinical manifestations have been described in heterozygous individuals

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP4V2 gene.

  • not_provided (400 variants)
  • Bietti_crystalline_corneoretinal_dystrophy (90 variants)
  • Retinal_dystrophy (55 variants)
  • Inborn_genetic_diseases (50 variants)
  • Corneal_dystrophy (36 variants)
  • CYP4V2-related_disorder (5 variants)
  • not_specified (4 variants)
  • Retinitis_pigmentosa (3 variants)
  • Optic_atrophy (2 variants)
  • Choroideremia (1 variants)
  • Corneal_Dystrophy,_Recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4V2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000207352.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
4
clinvar
76
clinvar
3
clinvar
 84
missense
15
clinvar
13
clinvar
216
clinvar
10
clinvar
1
clinvar
 255
nonsense
14
clinvar
4
clinvar
 18
start loss
0
frameshift
19
clinvar
5
clinvar
 24
splice donor/acceptor (+/-2bp)
9
clinvar
7
clinvar
1
clinvar
 17
Total 58 29 221 86 4

Highest pathogenic variant AF is 0.000110285

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CYP4V2protein_codingprotein_codingENST00000378802 1121937
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.20e-100.66312557601721257480.000684
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1213052991.020.00001663456
Missense in Polyphen112107.961.03741261
Synonymous0.919961080.8880.00000591966
Loss of Function1.421927.00.7050.00000129311

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009760.000976
Ashkenazi Jewish0.000.00
East Asian0.0009240.000925
Finnish0.001720.00171
European (Non-Finnish)0.0007480.000747
Middle Eastern0.0009240.000925
South Asian0.00006530.0000653
Other0.0006560.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Omega-hydroxylase that oxidizes medium-chain saturated fatty acids and polyunsaturated omega-3 fatty acids, and which plays a role in fatty acid and steroid metabolism in the eye (PubMed:19661213, PubMed:22772592). Catalyzes the omega- hydroxylation of medium-chain saturated fatty acids such as laurate, myristate and palmitate in an NADPH-dependent pathway. The substrate specificity is higher for myristate > laurate > palmitate (C14>C16>C12) (PubMed:19661213). Acts as a polyunsaturated omega-3 fatty acids hydroxylase by mediating oxidation of docosahexaenoate (DHA) to 22-hydroxydocosahexaenoate (PubMed:22772592). Also produces some 21-hydroxydocosahexaenoate. Also converts eicosapentaenoate (EPA) to 20- hydroxyeicosapentaenoate (20-OH-EPA) (PubMed:22772592). {ECO:0000269|PubMed:19661213, ECO:0000269|PubMed:22772592}.;
Pathway
Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Signaling by GPCR;Signal Transduction;Phase I - Functionalization of compounds;Endogenous sterols;Cytochrome P450 - arranged by substrate type;Biological oxidations;Metabolism;The canonical retinoid cycle in rods (twilight vision);G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.272

Intolerance Scores

loftool
0.535
rvis_EVS
0.42
rvis_percentile_EVS
77.23

Haploinsufficiency Scores

pHI
0.170
hipred
N
hipred_score
0.229
ghis
0.485

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.641

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cyp4v3
Phenotype
vision/eye phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
retinoid metabolic process;visual perception;fatty acid omega-oxidation;sterol metabolic process;response to stimulus
Cellular component
endoplasmic reticulum membrane;integral component of membrane
Molecular function
monooxygenase activity;iron ion binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;heme binding