FADS3

Summary

FADS3 (fatty acid desaturase 3, HGNC:3576) is a protein-coding gene on chromosome 11q12.2, encoding Fatty acid desaturase 3 (Q9Y5Q0). Mammals have different sphingoid bases that differ in their length and/or pattern of desaturation and hydroxyl groups.

The protein encoded by this gene is a member of the fatty acid desaturase (FADS) gene family. Desaturase enzymes regulate unsaturation of fatty acids through the introduction of double bonds between defined carbons of the fatty acyl chain. FADS family members are considered fusion products composed of an N-terminal cytochrome b5-like domain and a C-terminal multiple membrane-spanning desaturase portion, both of which are characterized by conserved histidine motifs. This gene is clustered with family members FADS1 and FADS2 at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization.

Source: NCBI Gene 3995 — RefSeq curated summary.

At a glance

• GWAS associations: 60
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_021727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3576
Approved symbol	FADS3
Name	fatty acid desaturase 3
Location	11q12.2
Locus type	gene with protein product
Status	Approved
Aliases	CYB5RP
Ensembl gene	ENSG00000221968
Ensembl biotype	protein_coding
OMIM	606150
Entrez	3995

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 25 protein_coding, 5 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000278829, ENST00000414624, ENST00000525094, ENST00000525588, ENST00000526294, ENST00000527379, ENST00000527697, ENST00000529404, ENST00000529525, ENST00000531956, ENST00000533676, ENST00000534223, ENST00000534426, ENST00000873458, ENST00000873459, ENST00000873460, ENST00000873461, ENST00000873462, ENST00000937848, ENST00000937849, ENST00000937850, ENST00000937851, ENST00000969790, ENST00000969791, ENST00000969792, ENST00000969793, ENST00000969794, ENST00000969795, ENST00000969796, ENST00000969797, ENST00000969798

RefSeq mRNA: 1 — MANE Select: NM_021727 NM_021727

CCDS: CCDS8013

Canonical transcript exons

ENST00000278829 — 12 exons

Exon	Start	End
ENSE00000990845	61876866	61876963
ENSE00000990846	61876359	61876455
ENSE00001315551	61891169	61891545
ENSE00002176319	61873526	61873865
ENSE00003469558	61879312	61879509
ENSE00003471838	61877511	61877587
ENSE00003551052	61878512	61878634
ENSE00003569857	61878746	61878847
ENSE00003589996	61880041	61880151
ENSE00003591508	61876111	61876190
ENSE00003605467	61875851	61875976
ENSE00003669316	61878155	61878215

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 98.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.9062 / max 893.9926, expressed in 1781 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120050	32.2921	1737
120048	3.7158	1403
120051	1.5002	1007
120049	1.2411	885
120047	0.5033	286
120043	0.3333	160
120045	0.2214	27
120044	0.0851	11
120046	0.0140	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibial nerve	UBERON:0001323	98.36	gold quality
ascending aorta	UBERON:0001496	98.20	gold quality
thoracic aorta	UBERON:0001515	98.18	gold quality
apex of heart	UBERON:0002098	98.12	gold quality
right coronary artery	UBERON:0001625	98.07	gold quality
left coronary artery	UBERON:0001626	98.03	gold quality
coronary artery	UBERON:0001621	97.96	gold quality
aorta	UBERON:0000947	97.94	gold quality
sural nerve	UBERON:0015488	97.82	gold quality
popliteal artery	UBERON:0002250	97.81	gold quality
tibial artery	UBERON:0007610	97.81	gold quality
descending thoracic aorta	UBERON:0002345	97.77	gold quality
omental fat pad	UBERON:0010414	97.29	gold quality
peritoneum	UBERON:0002358	97.24	gold quality
adipose tissue of abdominal region	UBERON:0007808	97.19	gold quality
left adrenal gland cortex	UBERON:0035825	96.93	gold quality
subcutaneous adipose tissue	UBERON:0002190	96.91	gold quality
left adrenal gland	UBERON:0001234	96.85	gold quality
right adrenal gland	UBERON:0001233	96.81	gold quality
adrenal cortex	UBERON:0001235	96.62	gold quality
adipose tissue	UBERON:0001013	96.61	gold quality
right adrenal gland cortex	UBERON:0035827	96.61	gold quality
heart left ventricle	UBERON:0002084	96.46	gold quality
cardiac ventricle	UBERON:0002082	96.27	gold quality
connective tissue	UBERON:0002384	96.04	gold quality
mucosa of stomach	UBERON:0001199	95.98	gold quality
trigeminal ganglion	UBERON:0001675	95.86	gold quality
right atrium auricular region	UBERON:0006631	95.64	gold quality
saphenous vein	UBERON:0007318	95.62	gold quality
olfactory bulb	UBERON:0002264	95.44	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	24.74
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting FADS3, 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-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-4707-3P	86.55	62.02	99

Literature-anchored findings (GeneRIF, showing 12)

• USF1 and FADS3 are causal candidate genes for the Mexican familial combined hyperlipidemia. (PMID:19750004)
• FADS3 does exist under multiple protein isoforms depending on the mammalian tissues. (PMID:19752397)
• it is highly likely that a gene product of FADS3 has desaturating activity. (PMID:21366865)
• Data suggest that FADS3 alternative transcripts/splicing are up-regulated in liver by dietary docosahexaenoic/arachidonic acids by peroxisome proliferator-activated receptor gamma (PPARg)-dependent mechanism unrelated to other desaturases (FADS1/2). (PMID:22398025)
• genetic association study in maternal/child dyads in England: Data suggest that SNPs in FADS3 (and in FADS1/FADS2) influence fetal fatty acid metabolism; both maternal and child FADS genotypes/haplotypes influence cord plasma long-chain fatty acids. (PMID:22877655)
• Minor allele homozygotes and heterozygotes of rs174455 in FADS3 gene had lower levels of 22:5 omega-3, 20:4 omega-6, and Delta5desaturase activity in patients with type 2 diabetes mellitus. (PMID:24985009)
• pairwise comparison showed that individuals major homozygous for the SNP rs1000778 in the FADS3 gene had lower concentrations of a-linolenic acid and linoleic acid in their breast milk (PMID:27269715)
• Data demonstrated that the rs1000778-G allele in the FADS3 gene is related to increased risk for coronary artery disease in the northern Chinese Han population. (PMID:28237083)
• FADS3 is a Delta14Z sphingoid base desaturase that contributes to gender differences in the human plasma sphingolipidome. (PMID:31862735)
• Biosynthesis of the anti-lipid-microdomain sphingoid base 4,14-sphingadiene by the ceramide desaturase FADS3. (PMID:31916624)
• Overexpression of fatty acid desaturase 3 predicts poor prognosis in head and neck squamous cell carcinoma. (PMID:36626435)
• Placental expression of Fatty Acid Desaturases 1, 2 and 3 in selected pregnancy pathologies. (PMID:36652541)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	fads2	ENSDARG00000019532
mus_musculus	Fads3	ENSMUSG00000024664
rattus_norvegicus	Fads3	ENSRNOG00000020385
caenorhabditis_elegans		WBGENE00001395
caenorhabditis_elegans		WBGENE00001396

Paralogs (3): FADS2 (ENSG00000134824), FADS1 (ENSG00000149485), FADS6 (ENSG00000172782)

Protein

Protein identifiers

Fatty acid desaturase 3 — Q9Y5Q0 (reviewed: Q9Y5Q0)

Alternative names: Delta(13) fatty acid desaturase

All UniProt accessions (7): Q9Y5Q0, E9PKP8, E9PPZ4, E9PQC2, E9PS00, H0YCN1, H0YED5

UniProt curated annotations — full annotation on UniProt →

Function. Mammals have different sphingoid bases that differ in their length and/or pattern of desaturation and hydroxyl groups. The predominant sphingoid base that comprises mammalian ceramides is sphing-4-enine (sphingosine or SPH) which has a trans (E) desaturation at carbon 4. FADS3 is a desaturase that introduces a cis (Z) double bond between carbon 14 and carbon 15 of the sphingoid base (also known as long chain base, LCB), producing LCBs such as sphinga-4,14-dienine (SPD, d18:2(4E,14Z)) from SPH. Prefers SPH-containing ceramides (N-acylsphing-4-enines) as substrates. Capable of metabolizing also the SPH in its free form. SPD ceramides occur widely in mammalian tissues and cells. Due to their unusual structure containing a cis double bond, SPD ceramides may have an opposite, negative role in lipid microdomain formation relative to conventional ceramides. Could be involved in the detoxification of 1-deoxy sphingolipids, by desaturating the cytotoxic 1-deoxysphinganine (1-deoxySA, m18:0), produced under pathological conditions, to 1-deoxysphingenine (1-deoxysphingosine, 1-deoxySO, m18:1). Although prefers SPH-containing ceramides (N-acylsphing-4-enines) as substrates, it also exhibits activity toward dihydrosphingosine-containing CERs (N-acylsphinganines) and produces 14Z-SPH-containing sphingolipids,which can be found in patients with DEGS1 mutations. Its desaturase mechanism involves an electron transfer facilitated by cytochrome b5. FADS3 also acts as a methyl-end fatty acyl coenzyme A (CoA) desaturase that introduces a cis double bond between the preexisting double bond and the terminal methyl group of the fatty acyl chain. Desaturates (11E)-octadecenoate (trans-vaccenoate, the predominant trans fatty acid in human milk) at carbon 13 to generate (11E,13Z)-octadecadienoate (also known as conjugated linoleic acid 11E,13Z-CLA).

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Highly expressed in various organs and tissues including liver, kidney, brain, lung, pancreas, testis, ovary and skeletal muscle (at protein level).

Domain organisation. The protein sequence includes a number of characteristic features of microsomal fatty acid desaturases including the three histidine boxes (these domains may contain the active site and/or be involved in metal ion binding), and the N-terminal cytochrome b5 domain containing the heme-binding motif, HPGG, similar to that of other fatty acid desaturases.

Pathway. Lipid metabolism; sphingolipid metabolism. Lipid metabolism; polyunsaturated fatty acid biosynthesis.

Miscellaneous. A 28 kDa isoform is expressed in lung, kidney, pancreas and ovary (at protein level).

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

RefSeq proteins (1): NP_068373* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001199	Cyt_B5-like_heme/steroid-bd	Domain
IPR005804	FA_desaturase_dom	Domain
IPR012171	Fatty_acid_desaturase	Family
IPR036400	Cyt_B5-like_heme/steroid_sf	Homologous_superfamily

Pfam: PF00173, PF00487

Enzyme classification (BRENDA):

• EC 1.14.19.30 — acyl-lipid (8-3)-desaturase (BRENDA: 22 organisms, 30 substrates, 39 inhibitors, 2 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
(8Z,11Z,14Z)-ICOSA-8,11,14-TRIENOYL-[GLYCEROLIPI	0.056	1
DIHOMO-GAMMA-LINOLENIC ACID	0.0245	1

Catalyzed reactions (Rhea), 6 shown:

• (11E)-octadecenoyl-CoA + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = (11E,13Z)-octadecadienoyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:46056)
• an N-acylsphing-4-enine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = an N-acyl-sphinga-4E,14Z-dienine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:63928)
• N-(hexanoyl)sphing-4-enine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = N-hexanoyl-sphinga-4E,14Z-dienine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:63940)
• sphing-4-enine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = sphinga-4E,14Z-dienine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:76483)
• N-acyl-1-deoxysphinganine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = N-acyl-1-deoxysphing-14Z-enine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:76487)
• an N-acylsphinganine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = an N-acylsphing-14Z-enine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:76563)

UniProt features (17 total): topological domain 5, transmembrane region 4, short sequence motif 3, sequence variant 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y5Q0-F1	94.43	0.94

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 151 (showing top): RNGTGGGC_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, RIZKI_TUMOR_INVASIVENESS_3D_DN, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, USF_C, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, BROWNE_HCMV_INFECTION_48HR_DN, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, MARTINEZ_RB1_TARGETS_UP, ONKEN_UVEAL_MELANOMA_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, GOBP_SPHINGOLIPID_METABOLIC_PROCESS

GO Biological Process (6): lipid metabolic process (GO:0006629), unsaturated fatty acid biosynthetic process (GO:0006636), sphingolipid metabolic process (GO:0006665), gene expression (GO:0010467), fatty acid metabolic process (GO:0006631), fatty acid biosynthetic process (GO:0006633)

GO Molecular Function (3): 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), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid metabolic process	2
primary metabolic process	1
fatty acid biosynthetic process	1
unsaturated fatty acid metabolic process	1
macromolecule biosynthetic process	1
monocarboxylic acid metabolic process	1
fatty acid metabolic process	1
lipid biosynthetic process	1
monocarboxylic acid biosynthetic process	1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	1
binding	1
catalytic activity	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

720 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FADS3	SCD	O00767	902
FADS3	CYB5B	O43169	901
FADS3	DEGS1	O15121	520
FADS3	FADS6	Q8N9I5	470
FADS3	SCD5	Q86SK9	448
FADS3	ELOVL3	Q9HB03	435
FADS3	ELOVL2	Q9NXB9	433
FADS3	ELOVL6	Q9H5J4	428
FADS3	OXSM	Q9NWU1	425
FADS3	FASN	P49327	416
FADS3	UGCG	Q16739	403
FADS3	ELOVL5	Q9NYP7	401
FADS3	CYB5D1	Q6P9G0	388
FADS3	CYB5R4	Q7L1T6	381
FADS3	CYB5A	P00167	379

IntAct

21 interactions, top by confidence:

A	B	Type	Score
DHRSX	FADS3	psi-mi:“MI:0915”(physical association)	0.560
TMEM186	SDC4	psi-mi:“MI:0914”(association)	0.530
FADS3	DHX16	psi-mi:“MI:0914”(association)	0.350
NS3	C15orf61	psi-mi:“MI:0914”(association)	0.350
FADS3	PEX7	psi-mi:“MI:0914”(association)	0.350
OR10H2	ABCD4	psi-mi:“MI:0914”(association)	0.350
FFAR1	SLC12A8	psi-mi:“MI:0914”(association)	0.350
GPR182	SLC12A8	psi-mi:“MI:0914”(association)	0.350
MFSD4A	UBXN8	psi-mi:“MI:0914”(association)	0.350
LPAR2	EI24	psi-mi:“MI:0914”(association)	0.350
FADS3	PGRMC2	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
POLD3	ESYT2	psi-mi:“MI:0914”(association)	0.350
ACKR3	PDE2A	psi-mi:“MI:0914”(association)	0.350
CXCR3	RIMOC1	psi-mi:“MI:0914”(association)	0.350
FADS3	CLPTM1	psi-mi:“MI:0914”(association)	0.350
TMEM169	PTGES3L-AARSD1	psi-mi:“MI:0914”(association)	0.350
SLC2A2	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC2A5	ESYT2	psi-mi:“MI:0914”(association)	0.350
DHRSX	FADS3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (54): ALG14 (Affinity Capture-MS), LRRC8A (Affinity Capture-MS), ERICH5 (Affinity Capture-MS), ZGPAT (Affinity Capture-MS), NAGPA (Affinity Capture-MS), FNDC3A (Affinity Capture-MS), IKBIP (Affinity Capture-MS), TMEM186 (Affinity Capture-MS), UBB (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), DHX16 (Affinity Capture-MS), C19orf26 (Affinity Capture-MS), YTHDF1 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), NEMF (Affinity Capture-MS)

ESM2 similar proteins: A0A0C5PRW9, A0A0C5Q309, A4FV48, A4IFP3, A4UVI1, A8MWK0, A9SIZ6, B2KKL4, B7SB91, B8R1K0, D8X2C5, G5ED44, G5EG11, G5EGN2, O04353, O44390, O60427, O74212, O95864, P07308, P13011, P13516, P32291, Q0VAX3, Q23221, Q3EBF7, Q43469, Q4R749, Q5REA7, Q64420, Q6DDK2, Q6P7B9, Q6T707, Q79EF1, Q86SK9, Q8ISS3, Q8K1P9, Q8S3C1, Q92038, Q920L1

Diamond homologs: A0A0C5PRW9, A4FV48, A4IFP3, A4UVI1, A8MWK0, B2KKL4, B7GCG7, B8MKR3, B8R1K0, C8VJR5, D8X2C5, O04354, O22704, O43169, O48845, O60427, O74875, O94391, O95864, P00167, P00168, P00169, P00170, P00171, P00172, P00173, P00174, P00175, P04166, P09437, P32953, P40312, P40934, P49096, P49097, P49098, P49099, P49100, P56395, P82291

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
FADS3	“down-regulates quantity”	“long-chain fatty acyl-CoA(4-)”	“chemical modification”
FADS3	“up-regulates quantity”	arachidonoyl-CoA	“chemical modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2138 predictions. Top by Δscore:

Variant	Effect	Δscore
11:61875845:CCTCA:C	donor_loss	1.0000
11:61875846:CTCA:C	donor_loss	1.0000
11:61875847:TCACC:T	donor_loss	1.0000
11:61875848:CACC:C	donor_loss	1.0000
11:61875849:A:AC	donor_gain	1.0000
11:61875850:C:CC	donor_gain	1.0000
11:61875850:CCT:C	donor_loss	1.0000
11:61875850:CCTGA:C	donor_gain	1.0000
11:61876104:CA:C	donor_gain	1.0000
11:61876109:A:AC	donor_gain	1.0000
11:61876110:C:CA	donor_gain	1.0000
11:61876187:CCAG:C	acceptor_gain	1.0000
11:61876188:CAGC:C	acceptor_gain	1.0000
11:61876191:C:CC	acceptor_gain	1.0000
11:61876195:C:CT	acceptor_gain	1.0000
11:61876196:G:T	acceptor_gain	1.0000
11:61876202:C:CT	acceptor_gain	1.0000
11:61876202:C:T	acceptor_gain	1.0000
11:61876203:G:T	acceptor_gain	1.0000
11:61876355:CCACC:C	donor_loss	1.0000
11:61876356:CACC:C	donor_loss	1.0000
11:61876357:A:T	donor_loss	1.0000
11:61876358:CCTGA:C	donor_loss	1.0000
11:61877584:CCGA:C	acceptor_gain	1.0000
11:61877585:CGA:C	acceptor_gain	1.0000
11:61877585:CGAC:C	acceptor_gain	1.0000
11:61877586:GA:G	acceptor_gain	1.0000
11:61877588:C:CC	acceptor_gain	1.0000
11:61878151:TCA:T	donor_loss	1.0000
11:61878152:CACTC:C	donor_loss	1.0000

AlphaMissense

2941 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:61876443:G:C	S332R	0.995
11:61876443:G:T	S332R	0.995
11:61876445:T:G	S332R	0.995
11:61878595:G:C	H222D	0.993
11:61878537:A:G	F241S	0.990
11:61878563:G:C	D232E	0.990
11:61878563:G:T	D232E	0.990
11:61878578:G:C	N227K	0.990
11:61878578:G:T	N227K	0.990
11:61878593:G:C	H222Q	0.990
11:61878593:G:T	H222Q	0.990
11:61876430:A:G	W337R	0.989
11:61876430:A:T	W337R	0.989
11:61876410:G:C	H343Q	0.988
11:61876410:G:T	H343Q	0.988
11:61876940:G:C	F303L	0.988
11:61876940:G:T	F303L	0.988
11:61876942:A:G	F303L	0.988
11:61878564:T:C	D232G	0.988
11:61876173:G:C	N366K	0.987
11:61876173:G:T	N366K	0.987
11:61878565:C:G	D232H	0.987
11:61878634:C:G	G209R	0.987
11:61876128:G:C	N381K	0.986
11:61876128:G:T	N381K	0.986
11:61876413:G:C	N342K	0.986
11:61876413:G:T	N342K	0.986
11:61878174:C:A	Q263H	0.986
11:61878174:C:G	Q263H	0.986
11:61878564:T:G	D232A	0.986

dbSNP variants (sampled 300 via entrez): RS1000133069 (11:61889410 G>A,C), RS1000704007 (11:61873501 G>A), RS1000778 (11:61887833 A>G,T), RS1000871037 (11:61876564 A>G), RS1000895943 (11:61883354 C>G), RS1000912039 (11:61884616 G>A,T), RS1001026327 (11:61884406 C>T), RS1001265639 (11:61878096 A>C), RS1001413011 (11:61877675 G>A,T), RS1001426352 (11:61884005 T>C), RS1001457558 (11:61883706 G>A,C), RS1001540134 (11:61890455 T>G), RS1001644082 (11:61889620 C>T), RS1002011263 (11:61889815 G>A), RS1002221165 (11:61882230 C>T)

Disease associations

OMIM: gene MIM:606150 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

60 associations (top):

Study	Trait	p-value
GCST000282_5	LDL cholesterol	4.000000e-13
GCST000285_8	Cholesterol, total	2.000000e-10
GCST000286_8	Triglycerides	2.000000e-14
GCST000288_1	HDL cholesterol	4.000000e-06
GCST000290_6	HDL cholesterol	2.000000e-12
GCST000493_2	Sphingolipid levels	7.000000e-13
GCST000635_4	Response to statin therapy	3.000000e-06
GCST000755_2	HDL cholesterol	2.000000e-22
GCST000758_8	Triglycerides	5.000000e-24
GCST000759_17	LDL cholesterol	1.000000e-21
GCST000760_25	Cholesterol, total	2.000000e-22
GCST001178_7	Plasma omega-3 polyunsaturated fatty acid level (eicosapentaenoic acid)	7.000000e-28
GCST001179_6	Plasma omega-3 polyunsaturated fatty acid levels (docosapentaenoic acid)	3.000000e-60
GCST001180_7	Plasma omega-3 polyunsaturated fatty acid levels (alphalinolenic acid)	4.000000e-25
GCST001392_7	Lipid metabolism phenotypes	8.000000e-262
GCST001413_3	Sphingolipid levels	2.000000e-14
GCST001414_10	Phospholipid levels (plasma)	1.000000e-203
GCST001639_25	Metabolite levels	4.000000e-264
GCST001834_5	Oleic acid (18:1n-9) levels	2.000000e-32
GCST001840_3	Stearic acid (18:0) levels	1.000000e-20
GCST001852_1	Metabolite levels	3.000000e-09
GCST002216_25	Triglycerides	7.000000e-38
GCST002221_47	Cholesterol, total	3.000000e-37
GCST002222_53	LDL cholesterol	2.000000e-39
GCST002223_30	HDL cholesterol	8.000000e-28
GCST002318_107	Rheumatoid arthritis	2.000000e-08
GCST002444_5	Plasma omega-6 polyunsaturated fatty acid levels (dihomo-gamma-linolenic acid)	5.000000e-168
GCST002446_1	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	4.000000e-274
GCST002446_7	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	3.000000e-21
GCST002448_6	Plasma omega-6 polyunsaturated fatty acid levels (adrenic acid)	4.000000e-140

EFO canonical traits (19, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004574	total cholesterol measurement
EFO:0004530	triglyceride measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0007760	eicosapentaenoic acid measurement
EFO:0006809	docosapentaenoic acid measurement
EFO:0007759	alpha-linolenic acid measurement
EFO:0004529	lipid measurement
EFO:0004723	coronary artery calcification
EFO:0004471	insulin sensitivity measurement
EFO:0005680	omega-6 polyunsaturated fatty acid measurement
EFO:0006808	arachidonic acid measurement
EFO:1002011	adult onset asthma
EFO:0009963	bipolar I disorder
EFO:0004531	urate measurement
EFO:0010364	lysophosphatidylcholine 20:5 measurement
EFO:0010348	cholesteryl ester 20:4 measurement
EFO:0010437	triacylglycerol 58:10 measurement
EFO:0010386	phosphatidylcholine 38:4 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

55 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	6
Benzo(a)pyrene	increases expression	5
Valproic Acid	increases methylation, affects expression, increases expression	5
bisphenol A	decreases expression, increases expression, affects expression, affects cotreatment, increases methylation	4
Aflatoxin B1	affects expression, increases expression	4
Acetaminophen	increases expression	3
Arsenic	affects cotreatment, increases abundance, increases expression	2
Dactinomycin	increases expression, affects cotreatment	2
Cyclosporine	increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
sodium arsenate	increases abundance, increases expression	1
arsenite	increases expression, increases abundance	1
mono-(2-ethylhexyl)phthalate	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	decreases expression	1
monomethylarsonic acid	increases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
arsenic acid	increases abundance, increases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
cupric chloride	increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
monomethylarsonous acid	increases expression	1
K 7174	increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1
nutlin 3	affects cotreatment, increases expression	1
dimethylmonothioarsinic acid	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
jinfukang	increases expression, affects cotreatment	1

Clinical trials (associated diseases)

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