FASN

fatty acid synthase, the group of 7BS orphan methyltransferases|Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 17:82078337-82098294

Links

ENSG00000169710 ∙ NCBI:2194 ∙ OMIM:600212 ∙ HGNC:3594 ∙ Uniprot:P49327 ∙ 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 FASN gene.

• Epileptic encephalopathy (1850 variants)
• Inborn genetic diseases (107 variants)
• not provided (42 variants)
• FASN-related condition (9 variants)
• not specified (4 variants)
• Seizure (2 variants)
• 8 conditions (1 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FASN 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			25	581	50	656
missense			801	45	20	866
nonsense			2			2
start loss						0
frameshift			8			8
inframe indel			11			11
splice donor/acceptor (+/-2bp)			3			3
splice region			29	85	9	123
non coding			4	197	27	228
Total	0	0	854	823	97

Variants in FASN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-82079153-C-T		Epileptic encephalopathy	Uncertain significance (Dec 19, 2023)
17-82079158-G-A		Epileptic encephalopathy	Likely benign (Apr 20, 2020)
17-82079163-C-T		Epileptic encephalopathy • not specified	Uncertain significance (Apr 03, 2023)
17-82079164-G-A		Epileptic encephalopathy	Likely benign (Jan 13, 2023)
17-82079166-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-82079182-G-A		Epileptic encephalopathy	Likely benign (Sep 26, 2023)
17-82079183-C-A		Epileptic encephalopathy	Uncertain significance (Jun 29, 2023)
17-82079188-G-T		Epileptic encephalopathy • FASN-related disorder	Likely benign (Nov 27, 2023)
17-82079212-G-A		Epileptic encephalopathy	Likely benign (Oct 11, 2022)
17-82079230-C-T		Epileptic encephalopathy	Likely benign (Sep 05, 2023)
17-82079234-C-T		Epileptic encephalopathy • not specified	Uncertain significance (Aug 04, 2023)
17-82079235-G-A		Epileptic encephalopathy	Uncertain significance (Sep 22, 2023)
17-82079236-G-A		Epileptic encephalopathy	Likely benign (Nov 11, 2020)
17-82079247-C-T		Epileptic encephalopathy	Uncertain significance (Jul 16, 2023)
17-82079248-G-A		Epileptic encephalopathy	Likely benign (Nov 09, 2023)
17-82079253-C-T		Epileptic encephalopathy	Uncertain significance (Sep 21, 2023)
17-82079254-G-A		Epileptic encephalopathy	Likely benign (Oct 22, 2022)
17-82079259-C-T		Epileptic encephalopathy	Uncertain significance (Nov 13, 2020)
17-82079271-C-G		Epileptic encephalopathy	Uncertain significance (Aug 20, 2021)
17-82079271-C-T		Epileptic encephalopathy	Uncertain significance (Jan 10, 2024)
17-82079272-G-A		Epileptic encephalopathy • FASN-related disorder	Likely benign (Jan 15, 2024)
17-82079275-G-A		Epileptic encephalopathy	Likely benign (Jun 20, 2023)
17-82079280-C-T		Epileptic encephalopathy	Uncertain significance (Sep 17, 2023)
17-82079287-G-A		Epileptic encephalopathy	Likely benign (Aug 10, 2023)
17-82079288-G-T		Epileptic encephalopathy	Likely benign (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FASN	protein_coding	protein_coding	ENST00000306749	42	19995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.83e-11	125176	0	20	125196	0.0000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	1302	1.57e+3	0.832	0.000116	15928
Missense in Polyphen		283	557.4	0.50772		5804
Synonymous	-6.79	989	752	1.32	0.0000621	5338
Loss of Function	8.82	10	110	0.0911	0.00000577	1158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000382	0.000364
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000536	0.0000462
European (Non-Finnish)	0.0000664	0.0000620
Middle Eastern	0.00	0.00
South Asian	0.000136	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Fatty acid synthetase catalyzes the formation of long- chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. This multifunctional protein has 7 catalytic activities as an acyl carrier protein.
• Pathway: AMPK signaling pathway - Homo sapiens (human);Fatty acid biosynthesis - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Fatty Acid Biosynthesis;AMP-activated Protein Kinase (AMPK) Signaling;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;SREBF and miR33 in cholesterol and lipid homeostasis;Activation of gene expression by SREBF (SREBP);Liver X Receptor Pathway;Nuclear Receptors Meta-Pathway;Fatty Acid Biosynthesis;fig-met-1-last-solution;Angiopoietin Like Protein 8 Regulatory Pathway;Lipid Metabolism Pathway;Liver steatosis AOP;Steatosis AOP;Pathways in clear cell renal cell carcinoma;Metabolism of lipids;Fatty acyl-CoA biosynthesis;Regulation of cholesterol biosynthesis by SREBP (SREBF);Metabolism;p73 transcription factor network;Fatty acid metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of steroids;palmitate biosynthesis;Metabolism of vitamins and cofactors;fatty acid biosynthesis initiation;fatty acid elongation -- saturated;Activation of gene expression by SREBF (SREBP);Validated transcriptional targets of deltaNp63 isoforms (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.0279
• rvis_EVS: -3.39
• rvis_percentile_EVS: 0.38

Haploinsufficiency Scores

• pHI: 0.567
• hipred: Y
• hipred_score: 0.745
• ghis: 0.541

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fasn
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs 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); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: osteoblast differentiation;acetyl-CoA metabolic process;fatty acid metabolic process;fatty acid biosynthetic process;ether lipid biosynthetic process;neutrophil differentiation;monocyte differentiation;mammary gland development;positive regulation of cellular metabolic process;macromolecule metabolic process;regulation of cholesterol biosynthetic process;fatty-acyl-CoA biosynthetic process;oxidation-reduction process;cellular response to interleukin-4;establishment of endothelial intestinal barrier
• Cellular component: Golgi apparatus;cytosol;plasma membrane;membrane;melanosome;glycogen granule;extracellular exosome
• Molecular function: RNA binding;fatty acid synthase activity;[acyl-carrier-protein] S-acetyltransferase activity;[acyl-carrier-protein] S-malonyltransferase activity;3-oxoacyl-[acyl-carrier-protein] synthase activity;3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity;oleoyl-[acyl-carrier-protein] hydrolase activity;protein binding;drug binding;(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity;myristoyl-[acyl-carrier-protein] hydrolase activity;palmitoyl-[acyl-carrier-protein] hydrolase activity;phosphopantetheine binding;protein homodimerization activity;cadherin binding;enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity;3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity;NADPH binding;3-oxo-glutaryl-[acp] methyl ester reductase activity;3-oxo-pimeloyl-[acp] methyl ester reductase activity