ELOVL1
ELOVL fatty acid elongase 1, the group of MicroRNA protein coding host genes
Basic information
Region (hg38): 1:43363398-43368074
Links
Phenotypes
GenCC
Source:
- ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features (Limited), mode of inheritance: AD
- ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features (Strong), mode of inheritance: AD
- ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features (Strong), mode of inheritance: AD
- ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facies | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dermatologic; Neurologic; Ophthalmologic | 29496980; 30487246 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (50 variants)
- not_specified (14 variants)
- ELOVL1-related_disorder (5 variants)
- Ichthyotic_keratoderma,_spasticity,_hypomyelination,_and_dysmorphic_facial_features (2 variants)
- Optic_atrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELOVL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022821.4. 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 | 17 | 19 | ||||
| missense | 25 | 29 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 2 | 0 | 26 | 19 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ELOVL1 | protein_coding | protein_coding | ENST00000372458 | 7 | 4629 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.679 | 0.321 | 125741 | 0 | 3 | 125744 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.81 | 94 | 158 | 0.595 | 0.00000882 | 1831 |
| Missense in Polyphen | 36 | 79.208 | 0.4545 | 950 | ||
| Synonymous | -1.72 | 74 | 57.4 | 1.29 | 0.00000318 | 529 |
| Loss of Function | 3.12 | 3 | 16.8 | 0.179 | 8.14e-7 | 175 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| 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 that exhibits activity toward saturated C18 to C26 acyl-CoA substrates, with the highest activity towards C22:0 acyl-CoA. May participate in the production of both saturated and monounsaturated VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators. Important for saturated C24:0 and monounsaturated C24:1 sphingolipid synthesis. Indirectly inhibits RPE65 via production of VLCFAs. {ECO:0000255|HAMAP-Rule:MF_03201, ECO:0000269|PubMed:20166112, ECO:0000269|PubMed:20937905}.;
- Pathway
- Fatty acid elongation - Homo sapiens (human);stearate biosynthesis;Metabolism of lipids;Fatty acyl-CoA biosynthesis;alpha-linolenic acid (ALA) metabolism;Linoleic acid (LA) metabolism;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;Omega-3 fatty acid metabolism;Metabolism;Fatty acid metabolism;Omega-6 fatty acid metabolism;De novo fatty acid biosynthesis;Synthesis of very long-chain fatty acyl-CoAs
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.414
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.498
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.545
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.815
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Elovl1
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- elovl1a
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- increased curvature
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
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;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