EPHX3

epoxide hydrolase 3, the group of Abhydrolase domain containing

Basic information

Region (hg38): 19:15226919-15233435

Previous symbols: [ "ABHD9" ]

Links

ENSG00000105131 ∙ NCBI:79852 ∙ OMIM:617400 ∙ HGNC:23760 ∙ Uniprot:Q9H6B9 ∙ 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 EPHX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHX3 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				2	1	3
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	1

Variants in EPHX3

This is a list of pathogenic ClinVar variants found in the EPHX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15227512-C-T			Likely benign (Jul 01, 2022)
19-15227547-C-A		not specified	Uncertain significance (May 17, 2023)
19-15227553-C-A		not specified	Uncertain significance (May 17, 2023)
19-15227559-G-A		not specified	Uncertain significance (Apr 25, 2024)
19-15227590-C-A		not specified	Likely benign (May 03, 2023)
19-15227612-C-A		not specified	Uncertain significance (Nov 10, 2022)
19-15227627-G-A		not specified	Uncertain significance (Mar 13, 2023)
19-15227778-G-A		not specified	Uncertain significance (May 21, 2024)
19-15227836-G-C		not specified	Uncertain significance (Nov 14, 2023)
19-15227850-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-15227883-G-A		not specified	Uncertain significance (Oct 20, 2021)
19-15228023-T-G		not specified	Uncertain significance (Mar 20, 2023)
19-15228026-C-T		not specified	Uncertain significance (Jul 28, 2021)
19-15228027-G-A			Likely benign (Oct 01, 2022)
19-15228067-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-15228068-G-A		not specified	Uncertain significance (May 27, 2022)
19-15228089-G-A		not specified	Uncertain significance (Jun 07, 2024)
19-15230973-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-15230986-C-T		not specified	Uncertain significance (Nov 06, 2023)
19-15231003-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-15231052-C-T		not specified	Uncertain significance (May 15, 2023)
19-15231073-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-15231263-T-C		not specified	Uncertain significance (Jan 26, 2022)
19-15231284-T-G		not specified	Uncertain significance (Nov 03, 2022)
19-15231316-G-C		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHX3	protein_coding	protein_coding	ENST00000221730	7	6517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.65e-15	0.00366	125673	0	66	125739	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0254	215	214	1.00	0.0000121	2294
Missense in Polyphen		49	50.154	0.97699		550
Synonymous	-0.305	98	94.2	1.04	0.00000522	768
Loss of Function	-0.623	21	18.1	1.16	0.00000102	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000913	0.000912
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000283	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000233	0.000229
Middle Eastern	0.000283	0.000272
South Asian	0.000490	0.000490
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of epoxide-containing fatty acids. Active in vitro against epoxyeicosatrienoic acids (EETs) including 8,9-EET, 9,10-EET, 11,12-EET and 14,15-EET and leukotoxin. {ECO:0000269|PubMed:22798687}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.954
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.603
• hipred: N
• hipred_score: 0.208
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.272

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ephx3
• Phenotype: normal phenotype

Gene ontology

• Biological process: lipid metabolic process;epoxide metabolic process
• Cellular component: endoplasmic reticulum;membrane;integral component of membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: epoxide hydrolase activity