ECHDC1
Basic information
Region (hg38): 6:127288712-127343609
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 17 | 18 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 2 | |||||
Total | 0 | 2 | 18 | 0 | 0 |
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) | ||
6-127289906-A-G | not specified | Uncertain significance (Sep 27, 2024) | ||
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) | ||
6-127327063-G-A | not specified | Uncertain significance (Dec 03, 2024) | ||
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) | ||
6-127330907-A-G | not specified | Uncertain significance (Nov 15, 2024) | ||
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:
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:
- 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
- Phenotype
Gene ontology
- Biological process
- fatty acid beta-oxidation
- Cellular component
- cytosol
- Molecular function
- enoyl-CoA hydratase activity;carboxy-lyase activity