ELOVL5

ELOVL fatty acid elongase 5

Basic information

Region (hg38): 6:53267397-53349179

Previous symbols: [ "SCA38" ]

Links

ENSG00000012660 ∙ NCBI:60481 ∙ OMIM:611805 ∙ HGNC:21308 ∙ Uniprot:Q9NYP7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia type 38 (Moderate), mode of inheritance: AD
• spinocerebellar ataxia type 38 (Strong), mode of inheritance: AD
• spinocerebellar ataxia type 38 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 39	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	Neurologic	25065913

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELOVL5 gene.

• not provided (72 variants)
• Inborn genetic diseases (12 variants)
• Spinocerebellar ataxia type 38 (8 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELOVL5 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				3	4	7
missense			32	3	1	36
nonsense				1		1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding			2	15	22	39
Total	0	0	37	22	27

Variants in ELOVL5

This is a list of pathogenic ClinVar variants found in the ELOVL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-53269050-T-C			Likely benign (May 23, 2021)
6-53269136-C-CCG		not specified	Uncertain significance (Jul 08, 2022)
6-53269156-C-T			Conflicting classifications of pathogenicity (Nov 06, 2023)
6-53269166-C-A			Benign/Likely benign (Jan 29, 2024)
6-53269166-CA-C			Uncertain significance (Mar 01, 2020)
6-53269171-G-T		Inborn genetic diseases	Uncertain significance (Aug 19, 2023)
6-53269185-G-A			Uncertain significance (Dec 11, 2023)
6-53269222-G-A			Uncertain significance (Oct 16, 2023)
6-53269224-T-C			Uncertain significance (Apr 07, 2022)
6-53269237-C-T		Inborn genetic diseases	Uncertain significance (Mar 23, 2018)
6-53269245-C-T			Benign (Oct 13, 2023)
6-53269247-G-A			Likely benign (Apr 05, 2023)
6-53269248-G-A		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
6-53269256-T-C			Likely benign (Apr 16, 2022)
6-53269306-C-CACAG			Benign (Sep 25, 2019)
6-53269366-C-CCTTTT			Benign (Sep 25, 2019)
6-53269450-C-CT			Likely benign (May 12, 2021)
6-53269503-A-G			Benign (Jun 05, 2021)
6-53270591-A-G			Uncertain significance (Oct 03, 2023)
6-53270647-G-T			Uncertain significance (Jun 21, 2022)
6-53270651-T-C		not specified • Spinocerebellar ataxia type 38	Conflicting classifications of pathogenicity (Dec 07, 2023)
6-53270655-A-G		Spinocerebellar ataxia type 38	Uncertain significance (Oct 18, 2019)
6-53270657-C-A		Spinocerebellar ataxia type 38	Uncertain significance (Sep 01, 2022)
6-53270660-C-A		Spinocerebellar ataxia type 38	Pathogenic (Aug 07, 2014)
6-53270677-C-T			Likely benign (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELOVL5	protein_coding	protein_coding	ENST00000541407	8	81752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.933	0.0666	125730	0	4	125734	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	127	185	0.686	0.0000101	2134
Missense in Polyphen		24	72.99	0.32881		898
Synonymous	1.54	53	69.3	0.765	0.00000386	603
Loss of Function	3.74	3	21.8	0.137	0.00000121	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• 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 acts specifically toward polyunsaturated acyl-CoA with the higher activity toward C18:3(n-6) acyl-CoA. May participate in the production of monounsaturated and of polyunsaturated 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_03205, ECO:0000269|PubMed:10970790, ECO:0000269|PubMed:20937905}.
• Pathway: Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);Alpha Linolenic Acid and Linoleic Acid Metabolism;miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;Metabolism of lipids;Fatty acyl-CoA biosynthesis;arachidonate biosynthesis III (metazoa);alpha-linolenic acid (ALA) metabolism;Linoleic acid (LA) metabolism;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;Metabolism;Fatty acid metabolism;icosapentaenoate biosynthesis II (metazoa);docosahexaenoate biosynthesis III (mammals);Synthesis of very long-chain fatty acyl-CoAs (Consensus)

Intolerance Scores

• loftool: 0.249
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.667
• hipred: Y
• hipred_score: 0.673
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0383

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elovl5
• Phenotype: reproductive system phenotype; liver/biliary system phenotype

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 fatty acid biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of endoplasmic reticulum membrane;dendrite;neuronal cell body;dendritic tree
• 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