ECHDC1

ethylmalonyl-CoA decarboxylase 1

Basic information

Region (hg38): 6:127288711-127343609

Links

ENSG00000093144 ∙ NCBI:55862 ∙ OMIM:612136 ∙ HGNC:21489 ∙ Uniprot:Q9NTX5 ∙ 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 ECHDC1 gene.

• Inborn genetic diseases (15 variants)
• Deficiency of butyryl-CoA dehydrogenase (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECHDC1 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		1	14			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1				1
non coding		1	1			2
Total	0	2	15	0	0

Highest pathogenic variant AF is 0.0000985

Variants in ECHDC1

This is a list of pathogenic ClinVar variants found in the ECHDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-127289885-C-T		not specified	Uncertain significance (Apr 13, 2023)
6-127289953-C-A		not specified	Uncertain significance (May 27, 2022)
6-127289961-C-T		not specified	Uncertain significance (Jul 26, 2022)
6-127290091-C-G		not specified	Uncertain significance (Jun 24, 2022)
6-127290161-A-G		not specified	Uncertain significance (Jul 14, 2021)
6-127290183-C-T		not specified	Uncertain significance (May 08, 2023)
6-127290200-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-127290246-C-T		not specified	Uncertain significance (Mar 29, 2022)
6-127290262-C-G		not specified	Uncertain significance (Oct 05, 2021)
6-127290309-ACTCT-A		Deficiency of butyryl-CoA dehydrogenase	Likely pathogenic (Sep 12, 2019)
6-127316477-A-G		Deficiency of butyryl-CoA dehydrogenase	Likely pathogenic (Sep 12, 2019)
6-127327010-T-C		not specified	Uncertain significance (Jan 23, 2023)
6-127327134-C-T		not specified	Uncertain significance (Jun 18, 2021)
6-127327136-T-C		not specified	Uncertain significance (Aug 23, 2021)
6-127327143-ACCTGC-TA		Deficiency of butyryl-CoA dehydrogenase	Likely pathogenic (Sep 12, 2019)
6-127331012-A-C		not specified	Uncertain significance (Apr 18, 2023)
6-127331017-A-T		not specified	Uncertain significance (Jul 20, 2021)
6-127342357-C-G		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECHDC1	protein_coding	protein_coding	ENST00000531967	6	54900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.60e-9	0.129	125623	0	118	125741	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.652	136	159	0.855	0.00000765	1993
Missense in Polyphen		34	45.093	0.754		534
Synonymous	-1.11	69	58.2	1.19	0.00000306	601
Loss of Function	0.138	13	13.5	0.960	5.73e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.00212	0.00212
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.00212	0.00212
South Asian	0.000495	0.000490
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Decarboxylases ethylmalonyl-CoA decarboxylase, a potentially toxic metabolite, to form butyryl-CoA, suggesting it might be involved in metabolite proofreading. Also has methylmalonyl-CoA decarboxylase activity at lower level. {ECO:0000269|PubMed:22016388}.
• Pathway: Propanoate metabolism - Homo sapiens (human);Fatty Acid Biosynthesis;Liver steatosis AOP (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.587
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.0848
• hipred: N
• hipred_score: 0.350
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0688

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Echdc1

Gene ontology

• Biological process: fatty acid beta-oxidation
• Cellular component: cytosol
• Molecular function: enoyl-CoA hydratase activity;carboxy-lyase activity