FADS1

fatty acid desaturase 1, the group of Fatty acid desaturases|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:61799626-61829318

Previous symbols: [ "LLCDL1" ]

Links

ENSG00000149485 ∙ NCBI:3992 ∙ OMIM:606148 ∙ HGNC:3574 ∙ Uniprot:O60427 ∙ 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 FADS1 gene.

• Inborn genetic diseases (5 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FADS1 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				2		2
missense			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	3	0

Variants in FADS1

This is a list of pathogenic ClinVar variants found in the FADS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61802839-C-A		not specified	Uncertain significance (Sep 06, 2022)
11-61812491-C-A		not specified	Uncertain significance (Aug 02, 2021)
11-61812622-C-T		not specified	Likely benign (Jan 31, 2022)
11-61812623-G-A		not specified	Uncertain significance (Aug 15, 2023)
11-61816744-C-A			Likely benign (Jul 26, 2018)
11-61816789-A-C			Likely benign (Jun 01, 2020)
11-61816814-G-C		not specified	Uncertain significance (May 11, 2022)
11-61816847-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-61828430-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FADS1	protein_coding	protein_coding	ENST00000350997	12	29692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.374	0.626	125667	0	11	125678	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.67	98	267	0.367	0.0000136	3288
Missense in Polyphen		26	94.661	0.27467		1176
Synonymous	1.56	88	109	0.810	0.00000564	976
Loss of Function	3.70	6	26.6	0.225	0.00000129	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.000169	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2 does not exhibit any catalytic activity toward 20:3n-6, but it may enhance FADS2 activity (By similarity). Isoform 1 is a component of a lipid metabolic pathway that catalyzes biosynthesis of highly unsaturated fatty acids (HUFA) from precursor essential polyunsaturated fatty acids (PUFA) linoleic acid (LA) (18:2n-6) and alpha-linolenic acid (ALA) (18:3n-3). Catalyzes the desaturation of dihomo-gamma-linoleic acid (DHGLA) (20:3n-6) and eicosatetraenoic acid (20:4n-3) to generate arachidonic acid (AA) (20:4n-6) and eicosapentaenoic acid (EPA)(20:5n-3), respectively. {ECO:0000250, ECO:0000269|PubMed:10601301, ECO:0000269|PubMed:10769175}.
• Pathway: Biosynthesis of unsaturated fatty acids - 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 leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;arachidonate biosynthesis III (metazoa);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;Linoleate metabolism;Omega-6 fatty acid metabolism;icosapentaenoate biosynthesis II (metazoa) (Consensus)

Recessive Scores

• pRec: 0.239

Intolerance Scores

• loftool: 0.562
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.693
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fads1
• Phenotype: immune system phenotype; digestive/alimentary 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); reproductive system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;unsaturated fatty acid biosynthetic process;cell-cell signaling;phospholipid biosynthetic process;cellular response to starvation;regulation of lipid metabolic process;alpha-linolenic acid metabolic process;linoleic acid metabolic process;regulation of cell differentiation;icosanoid biosynthetic process;oxidation-reduction process
• Cellular component: mitochondrion;endoplasmic reticulum membrane;membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: C-5 sterol desaturase activity;oxidoreductase activity;omega-6 fatty acid desaturase activity;acyl-CoA delta5-desaturase activity