FADS6

Summary

FADS6 (fatty acid desaturase 6, HGNC:30459) is a protein-coding gene on chromosome 17q25.1, encoding Fatty acid desaturase 6 (Q8N9I5).

Predicted to enable oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water. Predicted to be involved in lipid metabolic process. Predicted to be located in membrane.

Source: NCBI Gene 283985 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 65 total
• MANE Select transcript: NM_178128

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30459
Approved symbol	FADS6
Name	fatty acid desaturase 6
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000172782
Ensembl biotype	protein_coding
OMIM	620577
Entrez	283985

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 retained_intron

ENST00000413142, ENST00000579663, ENST00000612771, ENST00000621859, ENST00000921534, ENST00000958198

RefSeq mRNA: 1 — MANE Select: NM_178128 NM_178128

CCDS: CCDS54163

Canonical transcript exons

ENST00000612771 — 6 exons

Exon	Start	End
ENSE00001196583	74881068	74881255
ENSE00003718093	74882530	74882710
ENSE00003722328	74893352	74893633
ENSE00003732361	74892523	74892689
ENSE00003732647	74877302	74878477
ENSE00003739646	74879404	74879583

Expression profiles

Bgee: expression breadth broad, 91 present calls, max score 81.89.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3504 / max 28.7072, expressed in 143 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168021	0.3078	134
168020	0.0426	26

Top tissues by expression

114 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cerebellum	UBERON:0002037	81.89	gold quality
cerebellar hemisphere	UBERON:0002245	81.83	gold quality
cerebellar cortex	UBERON:0002129	81.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.75	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.53	gold quality
right adrenal gland cortex	UBERON:0035827	77.44	gold quality
duodenum	UBERON:0002114	77.26	gold quality
superior frontal gyrus	UBERON:0002661	76.72	gold quality
right adrenal gland	UBERON:0001233	75.77	gold quality
left adrenal gland	UBERON:0001234	75.69	gold quality
left adrenal gland cortex	UBERON:0035825	75.54	gold quality
prefrontal cortex	UBERON:0000451	75.00	gold quality
right lobe of liver	UBERON:0001114	74.22	gold quality
frontal cortex	UBERON:0001870	74.18	gold quality
skin of leg	UBERON:0001511	74.15	gold quality
primary visual cortex	UBERON:0002436	74.00	gold quality
zone of skin	UBERON:0000014	73.59	gold quality
skin of abdomen	UBERON:0001416	73.00	gold quality
Brodmann (1909) area 9	UBERON:0013540	72.68	gold quality
right frontal lobe	UBERON:0002810	72.64	gold quality
adrenal gland	UBERON:0002369	72.62	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.26	gold quality
liver	UBERON:0002107	71.93	gold quality
small intestine Peyer’s patch	UBERON:0003454	71.79	gold quality
lower esophagus mucosa	UBERON:0035834	70.93	gold quality
small intestine	UBERON:0002108	70.88	gold quality
cerebral cortex	UBERON:0000956	70.24	gold quality
anterior cingulate cortex	UBERON:0009835	69.70	gold quality
spleen	UBERON:0002106	69.63	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting FADS6, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-6088	99.29	68.45	1284
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-331-3P	98.76	64.91	793
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-6838-3P	98.40	65.88	559
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-6801-3P	98.04	64.64	805
HSA-MIR-6810-3P	97.96	64.57	1023
HSA-MIR-4708-5P	97.77	67.82	831
HSA-MIR-647	97.73	67.79	927
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-4540	96.90	67.46	473
HSA-MIR-431-5P	96.16	66.50	652
HSA-MIR-541-3P	96.07	66.11	1271
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-887-3P	94.03	63.71	71

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	FADS6	ENSDARG00000091503
mus_musculus	Fads6	ENSMUSG00000044788
rattus_norvegicus	Fads6	ENSRNOG00000021380
caenorhabditis_elegans		WBGENE00001395
caenorhabditis_elegans		WBGENE00001396

Paralogs (3): FADS2 (ENSG00000134824), FADS1 (ENSG00000149485), FADS3 (ENSG00000221968)

Protein

Protein identifiers

Fatty acid desaturase 6 — Q8N9I5 (reviewed: Q8N9I5)

All UniProt accessions (3): A0A087WWN9, A0A087WYB9, J3QRK6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Pathway. Lipid metabolism; fatty acid metabolism.

Similarity. Belongs to the fatty acid desaturase type 1 family.

RefSeq proteins (1): NP_835229* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005804	FA_desaturase_dom	Domain
IPR012171	Fatty_acid_desaturase	Family

Pfam: PF00487

UniProt features (18 total): transmembrane region 6, repeat 5, short sequence motif 3, region of interest 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9I5-F1	90.83	0.83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_FATTY_ACID_BIOSYNTHETIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOBP_FATTY_ACID_METABOLIC_PROCESS, ZHENG_IL22_SIGNALING_DN, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, PR_01, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY

GO Biological Process (3): lipid metabolic process (GO:0006629), fatty acid biosynthetic process (GO:0006633), fatty acid metabolic process (GO:0006631)

GO Molecular Function (2): oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water (GO:0016717), oxidoreductase activity (GO:0016491)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
fatty acid metabolic process	1
lipid biosynthetic process	1
monocarboxylic acid biosynthetic process	1
lipid metabolic process	1
monocarboxylic acid metabolic process	1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	1
catalytic activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1395 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FADS6	PYROXD1	Q8WU10	562
FADS6	FADS3	Q9Y5Q0	470
FADS6	FADS1	O60427	446
FADS6	FADS2	O95864	411
FADS6	SLCO1C1	Q9NYB5	405
FADS6	CREB3L4	Q8TEY5	402
FADS6	DEGS2	Q6QHC5	396
FADS6	ASS1	P00966	381
FADS6	GPAT2	Q6NUI2	377
FADS6	ACACA	Q13085	358
FADS6	MCHR1	Q99705	357
FADS6	FASN	P49327	357
FADS6	ALDH18A1	P54886	353
FADS6	GART	P22102	353
FADS6	CYB5R4	Q7L1T6	352

IntAct

62 interactions, top by confidence:

A	B	Type	Score
FADS6	TNS2	psi-mi:“MI:0915”(physical association)	0.560
FADS6	KRTAP1-5	psi-mi:“MI:0915”(physical association)	0.560
TNS2	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FADS6	MDFI	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	FADS6	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	FADS6	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FADS6	KRTAP3-3	psi-mi:“MI:0915”(physical association)	0.560
FADS6	INPP5K	psi-mi:“MI:0915”(physical association)	0.560
FADS6	PNKP	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	FADS6	psi-mi:“MI:0915”(physical association)	0.560
ARFIP2	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FADS6	PBX3	psi-mi:“MI:0915”(physical association)	0.560
GAD2	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FADS6	MTERF3	psi-mi:“MI:0915”(physical association)	0.560
TTPA	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FHL3	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FADS6	DIABLO	psi-mi:“MI:0915”(physical association)	0.560
UBASH3A	FADS6	psi-mi:“MI:0915”(physical association)	0.560
TRIM32	FADS6	psi-mi:“MI:0915”(physical association)	0.560
FADS6	TMEM14B	psi-mi:“MI:0915”(physical association)	0.560
FADS6	RCHY1	psi-mi:“MI:0915”(physical association)	0.370
FADS6	MDFI	psi-mi:“MI:0915”(physical association)	0.000
FADS6	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.000
FADS6	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000
FADS6	KRTAP6-3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (20): FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FADS6 (Two-hybrid), FHL3 (Two-hybrid), DIABLO (Two-hybrid), KRTAP10-8 (Two-hybrid), CYSRT1 (Two-hybrid)

ESM2 similar proteins: A0A194XK05, A0A6A6H402, A0A8F4NUZ8, A2VE15, A9ULE9, F4JMI5, F5H9I4, F5H9N9, F5HDD0, F5HE44, F5HE69, G5EEQ9, J7FIP9, J7FJH0, O30092, O42845, O83183, P03192, P03215, P09298, P09716, P09720, P09721, P0CU77, P0DW86, P0DW88, P0DW90, P0DXW1, P16733, P28948, P52373, P52542, P69334, P69335, P9WEG7, P9WEK8, Q01017, Q10436, Q17QW0, Q1HVE9

Diamond homologs: A2VE15, Q80UG1, Q8N9I5

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
FADS6	“down-regulates quantity”	“long-chain fatty acyl-CoA(4-)”	“chemical modification”
FADS6	“up-regulates quantity”	arachidonoyl-CoA	“chemical modification”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 21 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	5	19.9×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

65 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

936 predictions. Top by Δscore:

Variant	Effect	Δscore
17:74878474:TCAC:T	acceptor_gain	1.0000
17:74878475:CAC:C	acceptor_gain	1.0000
17:74878475:CACC:C	acceptor_gain	1.0000
17:74878476:ACCT:A	acceptor_loss	1.0000
17:74878478:C:CC	acceptor_gain	1.0000
17:74878478:CT:C	acceptor_loss	1.0000
17:74878479:T:A	acceptor_loss	1.0000
17:74878481:G:GC	acceptor_gain	1.0000
17:74881260:C:CT	acceptor_gain	1.0000
17:74881261:A:C	acceptor_gain	1.0000
17:74882525:CTCA:C	donor_loss	1.0000
17:74882526:TCACC:T	donor_loss	1.0000
17:74882528:A:AC	donor_gain	1.0000
17:74882529:C:CC	donor_gain	1.0000
17:74882529:C:G	donor_loss	1.0000
17:74882529:CCGA:C	donor_gain	1.0000
17:74882591:G:C	donor_gain	1.0000
17:74882706:CACAC:C	acceptor_gain	1.0000
17:74882711:CTA:C	acceptor_loss	1.0000
17:74882712:T:G	acceptor_loss	1.0000
17:74893346:CCTCA:C	donor_loss	1.0000
17:74893347:CTCA:C	donor_loss	1.0000
17:74893348:TCA:T	donor_loss	1.0000
17:74893349:CA:C	donor_loss	1.0000
17:74893351:C:CA	donor_loss	1.0000
17:74893351:CCTG:C	donor_gain	1.0000
17:74878473:TTCAC:T	acceptor_gain	0.9900
17:74878476:AC:A	acceptor_gain	0.9900
17:74878477:CCTGG:C	acceptor_gain	0.9900
17:74878481:G:C	acceptor_gain	0.9900

AlphaMissense

2394 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000064780 (17:74875569 C>A,T), RS1000190761 (17:74887236 G>A), RS1000192575 (17:74892434 C>T), RS1000194309 (17:74894791 C>A,T), RS1000422573 (17:74892417 C>T), RS1000453897 (17:74892209 T>C), RS1000510358 (17:74888157 C>A,G,T), RS1000587385 (17:74888460 G>A), RS1000590070 (17:74885664 C>T), RS1000649095 (17:74887662 A>G), RS1000684903 (17:74885325 A>C), RS1000756070 (17:74893721 G>A,T), RS1000788550 (17:74893540 A>G), RS1000843831 (17:74877267 G>C), RS1000909692 (17:74879970 T>C)

Disease associations

OMIM: gene MIM:620577 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
butyraldehyde	increases expression	1
abrine	increases expression	1
bisphenol S	decreases methylation	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Phthalic Acids	increases methylation	1
Triclosan	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.