ECHDC3

enoyl-CoA hydratase domain containing 3

Basic information

Region (hg38): 10:11742366-11764070

Links

ENSG00000134463 ∙ NCBI:79746 ∙ ∙ HGNC:23489 ∙ Uniprot:Q96DC8 ∙ 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 ECHDC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECHDC3 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in ECHDC3

This is a list of pathogenic ClinVar variants found in the ECHDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-11742599-G-A		not specified	Uncertain significance (Feb 22, 2025)
10-11742622-A-G		not specified	Uncertain significance (Aug 04, 2021)
10-11742661-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-11742683-C-G		not specified	Uncertain significance (Oct 05, 2023)
10-11742727-C-T		not specified	Uncertain significance (Feb 22, 2025)
10-11742740-G-C		not specified	Uncertain significance (Oct 29, 2024)
10-11742742-A-T		not specified	Uncertain significance (Mar 06, 2023)
10-11747420-A-T		not specified	Uncertain significance (May 14, 2024)
10-11747438-A-G		not specified	Uncertain significance (Jan 29, 2025)
10-11747443-A-G		not specified	Uncertain significance (Apr 22, 2022)
10-11747467-T-G		not specified	Uncertain significance (Mar 13, 2023)
10-11749516-C-T		not specified	Uncertain significance (Feb 27, 2023)
10-11749552-G-T		not specified	Uncertain significance (Feb 22, 2025)
10-11749569-G-A		not specified	Uncertain significance (Jan 07, 2025)
10-11755435-G-A		not specified	Uncertain significance (Mar 04, 2024)
10-11755439-C-G		not specified	Uncertain significance (Feb 14, 2025)
10-11755441-G-A		not specified	Likely benign (Jan 04, 2024)
10-11755477-G-A		not specified	Uncertain significance (Aug 23, 2021)
10-11755510-G-A		not specified	Uncertain significance (Jun 29, 2022)
10-11755519-G-A		not specified	Uncertain significance (Dec 13, 2022)
10-11755531-T-G		not specified	Uncertain significance (Mar 29, 2022)
10-11755534-G-A		not specified	Uncertain significance (Apr 13, 2023)
10-11755540-C-T		not specified	Uncertain significance (Dec 08, 2023)
10-11755553-T-C		not specified	Uncertain significance (May 05, 2023)
10-11763540-T-C		not specified	Likely benign (Oct 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECHDC3	protein_coding	protein_coding	ENST00000379215	5	21705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000476	0.244	125485	1	262	125748	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.190	166	159	1.04	0.00000957	1925
Missense in Polyphen		56	58.884	0.95102		671
Synonymous	0.0984	68	69.0	0.985	0.00000474	632
Loss of Function	-0.0563	8	7.83	1.02	3.30e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00778	0.00777
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000358	0.000352
Middle Eastern	0.000327	0.000326
South Asian	0.00333	0.00321
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.164

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.177
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.195

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Echdc3

Gene ontology

• Cellular component: mitochondrion
• Molecular function: catalytic activity