FADS3

fatty acid desaturase 3, the group of Fatty acid desaturases

Basic information

Region (hg38): 11:61873518-61892051

Previous symbols: [ "LLCDL3" ]

Links

ENSG00000221968 ∙ NCBI:3995 ∙ OMIM:606150 ∙ HGNC:3576 ∙ Uniprot:Q9Y5Q0 ∙ 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 FADS3 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FADS3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in FADS3

This is a list of pathogenic ClinVar variants found in the FADS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61873830-G-A		not specified	Uncertain significance (Jul 12, 2022)
11-61876169-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-61876366-C-G		not specified	Uncertain significance (Jun 02, 2023)
11-61876903-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-61878200-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-61878546-G-A		not specified	Uncertain significance (Jul 26, 2021)
11-61878552-G-A		not specified	Uncertain significance (Sep 19, 2023)
11-61879346-C-A		not specified	Uncertain significance (Aug 14, 2023)
11-61879442-C-T		not specified	Uncertain significance (May 16, 2022)
11-61879467-C-T		not specified	Uncertain significance (Dec 27, 2022)
11-61879508-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-61880049-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-61880072-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-61891272-T-G		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FADS3	protein_coding	protein_coding	ENST00000278829	12	18533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00253	0.997	125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	159	265	0.600	0.0000156	2893
Missense in Polyphen		67	117.7	0.56924		1263
Synonymous	1.40	101	121	0.837	0.00000829	849
Loss of Function	3.00	9	25.3	0.356	0.00000117	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000821	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Omega-3 fatty acid metabolism;Linoleate metabolism;Omega-6 fatty acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.501
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.581
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fads3
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: unsaturated fatty acid biosynthetic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: molecular_function;oxidoreductase activity