FADS2

fatty acid desaturase 2, the group of Fatty acid desaturases

Basic information

Region (hg38): 11:61792980-61867354

Previous symbols: [ "LLCDL2" ]

Links

ENSG00000134824 ∙ NCBI:9415 ∙ OMIM:606149 ∙ HGNC:3575 ∙ Uniprot:O95864 ∙ 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 FADS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FADS2 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					1	1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2	2	1	5
Total	0	0	8	2	2

Variants in FADS2

This is a list of pathogenic ClinVar variants found in the FADS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61795501-G-A		not specified	Uncertain significance (Oct 05, 2022)
11-61795593-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-61795654-C-T		not specified	Uncertain significance (Mar 17, 2023)
11-61795672-G-A		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
11-61795747-G-A		not specified	Uncertain significance (Jan 24, 2024)
11-61795930-T-C			Uncertain significance (Apr 08, 2021)
11-61796034-G-T		not specified	Uncertain significance (Jun 03, 2024)
11-61796065-G-A		Non-immune hydrops fetalis	Uncertain significance (Apr 29, 2021)
11-61796077-G-A		not specified	Uncertain significance (Mar 11, 2024)
11-61796217-C-G		not specified	Uncertain significance (Jun 16, 2024)
11-61796257-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-61796308-T-A		not specified	Uncertain significance (Sep 07, 2022)
11-61796325-C-T		not specified	Uncertain significance (Mar 22, 2022)
11-61796356-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-61796403-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-61796463-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-61802839-C-A		not specified	Uncertain significance (Sep 06, 2022)
11-61803420-C-A		not specified	Uncertain significance (Mar 19, 2024)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FADS2	protein_coding	protein_coding	ENST00000278840	12	74375

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00185	125744	0	3	125747	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.19	118	264	0.447	0.0000150	2974
Missense in Polyphen		9	57.676	0.15604		705
Synonymous	0.641	103	112	0.923	0.00000727	804
Loss of Function	4.48	2	27.2	0.0735	0.00000127	280

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	0.00	0.00
European (Non-Finnish)	0.00000901	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000375	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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 first and rate limiting step in this pathway which is the desaturation of LA (18:2n-6) and ALA (18:3n-3) into gamma- linoleic acid (GLA) (18:3n-6) and stearidonic acid (18:4n-3) respectively and other desaturation steps. Highly unsaturated fatty acids (HUFA) play pivotal roles in many biological functions. It catalizes as well the introduction of a cis double bond in palmitate to produce the mono-unsaturated fatty acid sapienate, the most abundant fatty acid in sebum. {ECO:0000269|PubMed:12713571, ECO:0000269|PubMed:9867867}.
• Pathway: Biosynthesis of unsaturated fatty acids - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Alpha Linolenic Acid and Linoleic Acid Metabolism;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;PPAR signaling pathway;Metabolism of lipids;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;γ-linolenate biosynthesis;Linoleate metabolism;Omega-6 fatty acid metabolism;icosapentaenoate biosynthesis II (metazoa);docosahexaenoate biosynthesis III (mammals) (Consensus)

Recessive Scores

• pRec: 0.278

Intolerance Scores

• loftool: 0.277
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.631
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fads2
• Phenotype: digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary 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); reproductive system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism 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

Gene ontology

• Biological process: unsaturated fatty acid biosynthetic process;alpha-linolenic acid metabolic process;linoleic acid metabolic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of plasma membrane;membrane
• Molecular function: stearoyl-CoA 9-desaturase activity;linoleoyl-CoA desaturase activity