FASN
fatty acid synthase, the group of 7BS orphan methyltransferases|Short chain dehydrogenase/reductase superfamily
Basic information
Region (hg38): 17:82078338-82098294
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- Epileptic_encephalopathy (2173 variants)
- not_specified (338 variants)
- not_provided (105 variants)
- FASN-related_disorder (82 variants)
- Thrombocytopenia (1 variants)
- Esotropia (1 variants)
- Tremor (1 variants)
- Finger_clinodactyly (1 variants)
- Autism_spectrum_disorder (1 variants)
- Hearing_impairment (1 variants)
- FASN-associated_disorder (1 variants)
- Clinodactyly (1 variants)
- Abnormal_facial_shape (1 variants)
- Midface_retrusion (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. These statistics are base on transcript: NM_000004104.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 14 | 708 | 43 | 765 | ||
| missense | 1034 | 65 | 18 | 1117 | ||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 11 | 11 | ||||
| splice donor/acceptor (+/-2bp) | 5 | |||||
| Total | 1 | 0 | 1066 | 773 | 61 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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