ELOVL3
Basic information
Region (hg38): 10:102226299-102229589
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (42 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELOVL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152310.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 39 | 42 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 39 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ELOVL3 | protein_coding | protein_coding | ENST00000370005 | 4 | 3262 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0188 | 0.906 | 125741 | 0 | 7 | 125748 | 0.0000278 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.746 | 129 | 155 | 0.831 | 0.00000807 | 1801 |
Missense in Polyphen | 44 | 55.225 | 0.79673 | 689 | ||
Synonymous | 0.331 | 57 | 60.3 | 0.946 | 0.00000335 | 508 |
Loss of Function | 1.51 | 4 | 8.83 | 0.453 | 3.78e-7 | 93 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000177 | 0.0000176 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the first and rate-limiting reaction of the four that constitute the long-chain fatty acids elongation cycle. This endoplasmic reticulum-bound enzymatic process, allows the addition of 2 carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. Condensing enzyme with higher activity toward C18 acyl-CoAs, especially C18:0 acyl-CoAs. May participate in the production of saturated and monounsaturated VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators. {ECO:0000255|HAMAP-Rule:MF_03203, ECO:0000269|PubMed:20937905}.;
- Pathway
- Fatty acid elongation - Homo sapiens (human);NR1D1 (REV-ERBA) represses gene expression;Circadian Clock;Metabolism of lipids;Fatty acyl-CoA biosynthesis;alpha-linolenic acid (ALA) metabolism;Linoleic acid (LA) metabolism;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;NR1D1 (REV-ERBA) represses gene expression;Metabolism;Fatty acid metabolism;Synthesis of very long-chain fatty acyl-CoAs
(Consensus)
Recessive Scores
- pRec
- 0.0923
Intolerance Scores
- loftool
- 0.675
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.56
Haploinsufficiency Scores
- pHI
- 0.0671
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.404
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.000995
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Elovl3
- Phenotype
- pigmentation phenotype; vision/eye phenotype; immune system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- unsaturated fatty acid biosynthetic process;fatty acid elongation, saturated fatty acid;sphingolipid biosynthetic process;fatty acid elongation, monounsaturated fatty acid;fatty acid elongation, polyunsaturated fatty acid;long-chain fatty-acyl-CoA biosynthetic process;alpha-linolenic acid metabolic process;very long-chain fatty acid biosynthetic process;linoleic acid metabolic process;positive regulation of cold-induced thermogenesis
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane
- Molecular function
- protein binding;fatty acid elongase activity;3-oxo-arachidoyl-CoA synthase activity;3-oxo-cerotoyl-CoA synthase activity;3-oxo-lignoceronyl-CoA synthase activity;very-long-chain 3-ketoacyl-CoA synthase activity