ECHDC2

enoyl-CoA hydratase domain containing 2

Basic information

Region (hg38): 1:52895909-52927212

Links

ENSG00000121310 ∙ NCBI:55268 ∙ ∙ HGNC:23408 ∙ Uniprot:Q86YB7 ∙ 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 ECHDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECHDC2 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in ECHDC2

This is a list of pathogenic ClinVar variants found in the ECHDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52896531-C-T		not specified	Uncertain significance (Jul 11, 2023)
1-52896545-C-T		not specified	Uncertain significance (Jun 09, 2022)
1-52896573-C-G		not specified	Uncertain significance (Feb 17, 2024)
1-52896578-C-T		not specified	Uncertain significance (Oct 27, 2023)
1-52897450-A-G		not specified	Uncertain significance (Jun 06, 2023)
1-52899181-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-52899190-A-G		not specified	Uncertain significance (Nov 16, 2021)
1-52899202-C-T		not specified	Uncertain significance (Feb 13, 2023)
1-52899212-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-52904668-A-G		not specified	Uncertain significance (Apr 01, 2024)
1-52904674-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-52904690-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-52904693-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-52904694-G-A		not specified	Likely benign (Apr 04, 2024)
1-52904744-G-A		not specified	Uncertain significance (Mar 01, 2024)
1-52905054-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-52906542-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-52906584-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-52907889-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-52911610-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-52911619-C-T		not specified	Likely benign (Sep 17, 2021)
1-52911755-G-A		not specified	Uncertain significance (Mar 23, 2023)
1-52921568-C-T		not specified	Uncertain significance (May 24, 2024)
1-52921616-C-T		not specified	Uncertain significance (Feb 17, 2024)
1-52921624-C-T		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECHDC2	protein_coding	protein_coding	ENST00000371522	10	31229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-10	0.206	124953	0	795	125748	0.00317

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0937	185	189	0.981	0.0000120	1810
Missense in Polyphen		82	90.464	0.90643		811
Synonymous	-0.141	79	77.4	1.02	0.00000462	658
Loss of Function	0.685	17	20.3	0.836	0.00000149	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00155
Ashkenazi Jewish	0.00318	0.00308
East Asian	0.00202	0.00201
Finnish	0.00129	0.00125
European (Non-Finnish)	0.00517	0.00502
Middle Eastern	0.00202	0.00201
South Asian	0.00236	0.00229
Other	0.00347	0.00343

dbNSFP

Source: dbNSFP

• Pathway: Fatty Acid Biosynthesis;Liver steatosis AOP;Butanoate metabolism (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.809
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.0834
• hipred: N
• hipred_score: 0.197
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Echdc2

Gene ontology

• Biological process: fatty acid beta-oxidation
• Cellular component: mitochondrion
• Molecular function: enoyl-CoA hydratase activity