ELOVL1

ELOVL fatty acid elongase 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:43363398-43368074

Links

ENSG00000066322 ∙ NCBI:64834 ∙ OMIM:611813 ∙ HGNC:14418 ∙ Uniprot:Q9BW60 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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: CGD

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 ClinVar and linked to the ELOVL1 gene.

• not provided (1 variants)
• Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features (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.

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				11	1	12
missense	1		21	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	4	1	7
non coding				3		3
Total	1	0	21	15	2

Variants in ELOVL1

This is a list of pathogenic ClinVar variants found in the ELOVL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-43363969-G-A			Likely benign (May 24, 2022)
1-43363979-C-T			Likely benign (Nov 05, 2024)
1-43363988-G-A			Likely benign (Jan 06, 2025)
1-43363988-G-T			Likely benign (Oct 25, 2024)
1-43363997-G-A			Likely benign (Nov 25, 2024)
1-43364032-T-C			Uncertain significance (Feb 24, 2024)
1-43364059-T-C			Likely benign (Aug 04, 2024)
1-43364087-G-C			Likely benign (Oct 22, 2024)
1-43364092-T-C		not specified	Uncertain significance (Jan 02, 2024)
1-43364108-G-T			Likely benign (Jan 06, 2025)
1-43364357-A-C			Likely benign (Oct 24, 2023)
1-43364420-C-T			Likely benign (Jul 12, 2024)
1-43364422-C-T			Uncertain significance (Oct 15, 2023)
1-43364423-G-A			Likely benign (Dec 06, 2024)
1-43364444-G-C			Uncertain significance (Sep 12, 2022)
1-43364448-G-A		Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facial features	Pathogenic (Jun 08, 2021)
1-43364450-G-A			Likely benign (Feb 24, 2024)
1-43364459-T-C			Likely benign (Nov 05, 2024)
1-43364468-T-A			Likely benign (Dec 10, 2024)
1-43364476-AAGAC-A			Likely benign (Jan 22, 2024)
1-43364531-TCAC-T			Likely benign (Oct 16, 2024)
1-43364549-A-C			Uncertain significance (Apr 29, 2023)
1-43364565-C-A		not specified	Uncertain significance (May 30, 2024)
1-43364565-C-G		not specified	Uncertain significance (Nov 04, 2024)
1-43364565-C-T		ELOVL1-related disorder	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

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: 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 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