ELOVL3

ELOVL fatty acid elongase 3

Basic information

Region (hg38): 10:102226299-102229589

Links

ENSG00000119915 ∙ NCBI:83401 ∙ OMIM:611815 ∙ HGNC:18047 ∙ Uniprot:Q9HB03 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELOVL3 gene.

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.

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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in ELOVL3

This is a list of pathogenic ClinVar variants found in the ELOVL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-102226561-A-G		not specified	Uncertain significance (Nov 10, 2022)
10-102226565-A-G		not specified	Uncertain significance (Aug 12, 2021)
10-102226567-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-102226568-T-G		not specified	Uncertain significance (Sep 22, 2022)
10-102227688-T-G		not specified	Uncertain significance (Dec 08, 2023)
10-102227726-A-G		not specified	Uncertain significance (Aug 11, 2022)
10-102228450-G-A		not specified	Uncertain significance (May 30, 2023)
10-102228461-T-C		not specified	Uncertain significance (Jan 02, 2024)
10-102228469-G-A		not specified	Uncertain significance (Dec 07, 2021)
10-102228472-G-A		not specified	Likely benign (Mar 25, 2024)
10-102228487-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-102228872-C-T		not specified	Uncertain significance (Jun 01, 2022)
10-102228888-G-T		not specified	Uncertain significance (Nov 07, 2022)
10-102228889-C-A		not specified	Uncertain significance (Jun 03, 2024)
10-102228899-G-A		not specified	Uncertain significance (Dec 19, 2022)
10-102228966-G-C		not specified	Uncertain significance (Nov 17, 2023)
10-102228986-A-G		not specified	Uncertain significance (Jan 31, 2023)
10-102229044-T-A		not specified	Uncertain significance (Jun 09, 2022)
10-102229124-T-C		not specified	Uncertain significance (Nov 07, 2023)
10-102229160-A-G		not specified	Likely benign (Jun 24, 2022)
10-102229169-A-G		not specified	Uncertain significance (Oct 16, 2023)
10-102229173-C-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

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: 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 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