ELOVL4
Basic information
Region (hg38): 6:79914814-79947553
Previous symbols: [ "STGD2", "STGD3", "SCA34" ]
Links
Phenotypes
GenCC
Source:
- congenital ichthyosis-intellectual disability-spastic quadriplegia syndrome (Definitive), mode of inheritance: AR
- spinocerebellar ataxia type 34 (Strong), mode of inheritance: AD
- spinocerebellar ataxia type 34 (Moderate), mode of inheritance: AD
- congenital ichthyosis-intellectual disability-spastic quadriplegia syndrome (Strong), mode of inheritance: AR
- Stargardt disease (Supportive), mode of inheritance: AD
- spinocerebellar ataxia type 34 (Supportive), mode of inheritance: AD
- congenital ichthyosis-intellectual disability-spastic quadriplegia syndrome (Supportive), mode of inheritance: AR
- Stargardt disease 3 (Definitive), mode of inheritance: AD
- congenital ichthyosis-intellectual disability-spastic quadriplegia syndrome (Strong), mode of inheritance: AR
- spinocerebellar ataxia type 34 (Strong), mode of inheritance: AD
- Stargardt disease 3 (Strong), mode of inheritance: AD
- Stargardt disease 3 (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Ichthyosis, spastic quadriplegia, and mental retardation; Spinocerebellar ataxia 34; Startgardt disease 3 | AD/AR | 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 | Biochemical; Dermatologic; Neurologic; Ophthalmologic | 10634627; 11726641; 11138005; 15557430; 22100072; 24566826 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (10 variants)
- Spinocerebellar ataxia type 34 (2 variants)
- ELOVL4-related disorder (1 variants)
- Stargardt disease 3;Congenital ichthyosis-intellectual disability-spastic quadriplegia syndrome;Spinocerebellar ataxia type 34 (1 variants)
- Stargardt disease 3 (1 variants)
- Retinal dystrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELOVL4 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 | 50 | 52 | ||||
missense | 99 | 107 | ||||
nonsense | 8 | |||||
start loss | 1 | |||||
frameshift | 9 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 1 | 6 | 5 | 1 | 13 | |
non coding | 36 | 28 | 33 | 97 | ||
Total | 11 | 9 | 142 | 80 | 35 |
Variants in ELOVL4
This is a list of pathogenic ClinVar variants found in the ELOVL4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-79914939-A-C | Stargardt disease 3 | Benign (Jan 12, 2018) | ||
6-79915040-T-C | Stargardt disease 3 | Uncertain significance (Jan 12, 2018) | ||
6-79915054-ATATGT-A | Stargardt Disease, Dominant | Uncertain significance (Jun 14, 2016) | ||
6-79915057-T-C | Stargardt disease 3 | Benign (Jan 12, 2018) | ||
6-79915097-C-T | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915102-T-C | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915185-T-C | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915367-A-C | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915415-A-G | Stargardt disease 3 | Uncertain significance (Jan 12, 2018) | ||
6-79915542-A-C | Stargardt disease 3 | Benign (Jan 13, 2018) | ||
6-79915558-T-C | Stargardt disease 3 | Benign (Jan 13, 2018) | ||
6-79915560-C-T | Stargardt disease 3 | Uncertain significance (Jan 12, 2018) | ||
6-79915570-T-C | Stargardt disease 3 | Uncertain significance (Jan 12, 2018) | ||
6-79915588-T-C | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915609-T-C | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915658-A-G | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915703-A-G | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79915805-A-G | Stargardt disease 3 | Uncertain significance (Jan 12, 2018) | ||
6-79915812-CAT-C | Stargardt Disease, Dominant | Benign (Jun 14, 2016) | ||
6-79915941-A-G | Stargardt disease 3 | Benign (Jan 13, 2018) | ||
6-79915999-C-T | Stargardt disease 3 | Benign (Jan 13, 2018) | ||
6-79916002-C-A | Stargardt disease 3 | Uncertain significance (Jan 13, 2018) | ||
6-79916099-G-A | Stargardt disease 3 | Benign (Jan 13, 2018) | ||
6-79916231-A-T | Stargardt disease 3 | Benign (Jan 13, 2018) | ||
6-79916235-T-A | Stargardt disease 3 | Uncertain significance (Jan 12, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ELOVL4 | protein_coding | protein_coding | ENST00000369816 | 6 | 32769 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.832 | 0.168 | 125736 | 0 | 12 | 125748 | 0.0000477 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.19 | 126 | 169 | 0.744 | 0.00000819 | 2068 |
Missense in Polyphen | 29 | 60.249 | 0.48134 | 735 | ||
Synonymous | -0.284 | 60 | 57.3 | 1.05 | 0.00000265 | 566 |
Loss of Function | 3.41 | 3 | 19.1 | 0.157 | 9.98e-7 | 198 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000466 | 0.0000462 |
European (Non-Finnish) | 0.0000704 | 0.0000703 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000163 | 0.000163 |
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 specifically elongates C24:0 and C26:0 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. May play a critical role in early brain and skin development. {ECO:0000255|HAMAP-Rule:MF_03204, ECO:0000269|PubMed:20937905}.;
- Disease
- DISEASE: Stargardt disease 3 (STGD3) [MIM:600110]: A common hereditary macular degeneration. It is characterized by decreased central vision, atrophy of the macula and underlying retinal pigment epithelium, and frequent presence of prominent flecks in the posterior pole of the retina. {ECO:0000269|PubMed:11138005, ECO:0000269|PubMed:11581213}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ichthyosis, spastic quadriplegia, and mental retardation (ISQMR) [MIM:614457]: A severe autosomal recessive disorder characterized by ichthyosis apparent from birth, profound psychomotor retardation with essentially no development, spastic quadriplegia, and seizures. {ECO:0000269|PubMed:22100072}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinocerebellar ataxia 34 (SCA34) [MIM:133190]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA34 is an autosomal dominant form characterized by the association of progressive cerebellar ataxia with erythrokeratodermia variabilis. {ECO:0000269|PubMed:24566826}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Fatty acid elongation - Homo sapiens (human);Alpha Linolenic Acid and Linoleic Acid Metabolism;Ectoderm Differentiation;Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;Synthesis of very long-chain fatty acyl-CoAs
(Consensus)
Recessive Scores
- pRec
- 0.0997
Intolerance Scores
- loftool
- 0.545
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 76.05
Haploinsufficiency Scores
- pHI
- 0.694
- hipred
- Y
- hipred_score
- 0.738
- ghis
- 0.445
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.144
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Elovl4
- 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); growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; 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); hematopoietic system phenotype; pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- fatty acid biosynthetic process;unsaturated fatty acid biosynthetic process;detection of visible light;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;very long-chain fatty acid biosynthetic process
- Cellular component
- endoplasmic reticulum;integral component of endoplasmic reticulum membrane
- Molecular function
- protein binding;G protein-coupled photoreceptor activity;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