SAA1

Summary

SAA1 (serum amyloid A1, HGNC:10513) is a protein-coding gene on chromosome 11p15.1, encoding Serum amyloid A-1 protein (P0DJI8). Major acute phase protein.

This gene encodes a member of the serum amyloid A family of apolipoproteins. The encoded preproprotein is proteolytically processed to generate the mature protein. This protein is a major acute phase protein that is highly expressed in response to inflammation and tissue injury. This protein also plays an important role in HDL metabolism and cholesterol homeostasis. High levels of this protein are associated with chronic inflammatory diseases including atherosclerosis, rheumatoid arthritis, Alzheimer’s disease and Crohn’s disease. This protein may also be a potential biomarker for certain tumors. Finally, antimicrobial activity against S. aureus and E. coli resides in the N-terminal portion of the mature protein. Alternate splicing results in multiple transcript variants that encode the same protein. A pseudogene of this gene is found on chromosome 11.

Source: NCBI Gene 6288 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 31 total
• Phenotypes (HPO): 32
• MANE Select transcript: NM_199161

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10513
Approved symbol	SAA1
Name	serum amyloid A1
Location	11p15.1
Locus type	gene with protein product
Status	Approved
Aliases	PIG4, TP53I4
Ensembl gene	ENSG00000173432
Ensembl biotype	protein_coding
OMIM	104750
Entrez	6288

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000356524, ENST00000405158, ENST00000532858, ENST00000649195, ENST00000689650

RefSeq mRNA: 3 — MANE Select: NM_199161 NM_000331, NM_001178006, NM_199161

CCDS: CCDS7835

Canonical transcript exons

ENST00000356524 — 4 exons

Exon	Start	End
ENSE00001210650	18269195	18269333
ENSE00001433067	18266264	18266296
ENSE00001729981	18266884	18266978
ENSE00002153675	18269717	18269967

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 99.50.

FANTOM5 (CAGE): breadth broad, TPM avg 41.7569 / max 26432.4763, expressed in 370 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113314	38.9994	309
113313	1.3573	162
113318	0.5502	30
113315	0.2904	12
206211	0.1437	13
113312	0.0723	38
206212	0.0696	8
113311	0.0682	6
206217	0.0493	5
206214	0.0370	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	99.50	gold quality
omental fat pad	UBERON:0010414	99.39	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	99.20	gold quality
thoracic mammary gland	UBERON:0005200	98.92	gold quality
saliva-secreting gland	UBERON:0001044	98.10	gold quality
liver	UBERON:0002107	98.06	gold quality
minor salivary gland	UBERON:0001830	97.99	gold quality
adipose tissue	UBERON:0001013	97.94	gold quality
right lung	UBERON:0002167	97.35	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.91	gold quality
subcutaneous adipose tissue	UBERON:0002190	96.67	gold quality
left coronary artery	UBERON:0001626	94.64	gold quality
right adrenal gland	UBERON:0001233	93.63	gold quality
vermiform appendix	UBERON:0001154	93.07	gold quality
right adrenal gland cortex	UBERON:0035827	92.96	gold quality
gastrocnemius	UBERON:0001388	92.23	gold quality
left uterine tube	UBERON:0001303	91.69	gold quality
ascending aorta	UBERON:0001496	91.55	gold quality
thoracic aorta	UBERON:0001515	91.50	gold quality
skin of abdomen	UBERON:0001416	91.34	gold quality
mucosa of stomach	UBERON:0001199	90.77	gold quality
tibial nerve	UBERON:0001323	90.48	gold quality
left adrenal gland	UBERON:0001234	90.46	gold quality
popliteal artery	UBERON:0002250	90.03	gold quality
tibial artery	UBERON:0007610	89.98	gold quality
skin of leg	UBERON:0001511	89.70	gold quality
right coronary artery	UBERON:0001625	89.62	gold quality
zone of skin	UBERON:0000014	89.49	gold quality
descending thoracic aorta	UBERON:0002345	89.47	gold quality
left adrenal gland cortex	UBERON:0035825	89.28	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-GEOD-130473	yes	30860.98
E-GEOD-86618	yes	797.48
E-GEOD-83139	yes	304.68
E-HCAD-9	yes	57.06
E-CURD-114	yes	31.86
E-HCAD-1	yes	14.34
E-MTAB-7249	yes	11.37
E-CURD-7	no	18703.08
E-ENAD-21	no	16129.61
E-CURD-11	no	7979.88
E-MTAB-10137	no	4659.42
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AHR, ATF5, CEBPA, CEBPB, CEBPD, CEBPG, CREB1, CTNNB1, GLI3, HNF4A, IRF6, NFKB1, NFKB, NR5A2, PGS1, RELA, SP1, STAT3, TFAP2A, TFCP2, YY1

miRNA regulators (miRDB)

4 targeting SAA1, 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-6752-3P	99.72	66.71	1587
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-660-5P	98.16	68.27	680
HSA-MIR-759	96.16	66.77	873

Literature-anchored findings (GeneRIF, showing 40)

• human platelets specifically adhere to SAA in an RGD- and alphaIIbbeta3-dependent manner, indicating a role for SAA in modulating platelet adhesion (PMID:11830469)
• relation to cholesterol metabolism and cardiovascular disease (REVIEW) (PMID:12056504)
• The endogenous SAA1 gene has a cytokine-driven transcriptional disadvantage compared to SAA2 that is superseded by a marginal transcriptional advantage when glucocorticoids are present. (PMID:12077270)
• the region containing the C/EBPalpha,beta consensus binding site between the bases -252 and -175 is important for the glucocorticoid-induced SAA1 gene expression in HASMCs but not in HepG2 cells (PMID:12410800)
• Data suggest that the frequency of the -13T serum amyloid A1 (SAA1) allele may explain the difference in prevalence of AA amyloidosis in Japanese and Caucasians. (PMID:12762135)
• Data show higher SAA1 homozygosity in familial Mediterranean fever (FMF)-amyloidosis patients than in FMF patients, but no significant difference between controls and FMF patients with and without amyloidosis for the TNF-alpha-308 G-A allele. (PMID:12762136)
• Results indicate a novel role for interleukin-18 in rheumatoid inflammation through the synovial serum amyloid A production. (PMID:14738910)
• Saa1 is regulated by tumor necrosis factor-alpha, interleukin-6 and glucocorticoids in hepatic and epithelial cells (PMID:14871291)
• Positive relationship between Tanis mRNA and the acute-phase protein serum amyloid A suggests an interaction between innate immune system responses and Tanis expression in muscle and adipose tissue. (PMID:15161744)
• SAA1a/a genotype is one genetic factor that confers a significant risk for amyloidosis in the Turkish FMF population but neither SAA1 nor SAA2 genotypes had a significant effect on SAA level. (PMID:15170927)
• The up-regulation of the A-SAA and FPRL1 genes in inflamed synovial tissue suggests an important role in the pathophysiology of inflammatory arthritis. (PMID:15188355)
• Human hepatocytes stimulated by Lipopolysaccharide produced serum amyloid A protein. (PMID:15225640)
• SR-BI plays a key role in SAA metabolism through its ability to interact with and internalize SAA and SAA influences HDL cholesterol metabolism through its inhibitory effects on SR-BI-mediated selective lipid uptake (PMID:15561721)
• SAA is expressed by subcutaneous white adipose tissue and its production at this site is regulated by nutritional status. (PMID:15729583)
• In this study, the SAA4 protein was examined in the high-density lipoprotein fraction of both healthy and diseased individuals. (PMID:15910745)
• Increased amyloid AA is associated with amyloidosis and familial Mediterranean fever (PMID:15972323)
• Serum amyloid A has a role in promoting cholesterol efflux mediated by scavenger receptor B-I (PMID:16120612)
• Within a subsample from the BELSTRESS study of 892 male subjects free of cardiovascular disease, dimensions of job stress from the job demand-control-support model were related to biomarkers of inflammation and infection. (PMID:16155472)
• We provide evidence that STAT3 plays an essential role in cytokine-driven SAA expression, although the human SAA gene shows no typical STAT3 response element. (PMID:16236134)
• Data show that serum amyloid A dissociates apolipoprotein E from high density lipoprotein in cerebrospinal fluid. (PMID:16651021)
• Increased expression of SAA1 by adipocytes in obesity may play a critical role in local and systemic inflammation and free fatty acid production and could be a direct link between obesity and its comorbidities. (PMID:16737350)
• serum amyloid A and C-reactive protein are expressed differently in exudates and transudates (PMID:16864904)
• binding of SAA to FPRL1 may contribute to the destruction of bone and cartilage via the promotion of synoviocyte hyperplasia and angiogenesis (PMID:17015746)
• the SAA1 alpha/alpha genotype is a risk factor for amyloidosis in BD (PMID:17039260)
• SAA induced TF mRNA in PBMC within 30 min and optimal procoagulant activity within 4 h through activation of NF-kappaB via the ERK1/2 and p38 MAPK pathways. SAA-induced TF was partially inhibited by high-density lipoprotein. (PMID:17237436)
• SAA reduces hepatitis C virus (HCV) infectivity in a dose-dependent manner when added during HCV infection but not after virus entry. (PMID:17329325)
• SAA can be used as a valuable indicator of disease activity in ankylosing spondylitis. (PMID:17461519)
• There is a relative deficiency of circulating cystatin C (CysC) in systemic inflammation in rheumatoid arthritis. Interaction between CysC and serum amyloid A protein explains this CysC deficiency and suggests CysC is regulating inflammatory responses. (PMID:17552057)
• SAA was quantitated using PVDF affinity probes and MALD-MS. (PMID:17676666)
• SSA1 protein was identified in the blood of colon neoplasm patients. (PMID:17806085)
• we first show that SAA1 (coding for the major SAA isoform) but not SAA2 transcripts are expressed in human trabecular and cortical bone fractions and bone marrow. (PMID:17849429)
• Analysis of SAA1 gene polymorphisms showed the rarity of the putative amyloidogenic -13T allele in Greek populations may be related to low prevalence of AA amyloidosis development in Greek RA patients. (PMID:17968686)
• The association between SAA and leptin suggests an interaction between these two adipokines, which may have implications in inflammatory processes related to obesity and the metabolic syndrome (PMID:18299466)
• The SAA-RAGE-stimulated NF-kappaB signaling pathway has an important role in the pathogenesis of rheumatoid arthritis. (PMID:18322992)
• fifth day of observation but were not good predictors of mortality in septic shock. (PMID:18385816)
• suggest a potential role for SAA in inflammatory diseases through activation of TLR2 (PMID:18566366)
• SAA is a prothrombotic and proinflammatory mediator in acute coronary syndrome which may contribute to atherogenesis and its complications (PMID:18571179)
• up-regulation of SAA protein expression mediates the inhibitory effect of Ganoderma lucidum polysaccharides on tumor cell adhesion to endothelial cells. (PMID:18695905)
• A review of how SAA contributes to tumour development and the acceleration of tumour progression and metastasis is presented. (PMID:18726069)
• SAA, an endogenous ligand of the chemokine formyl peptide receptor-like 1 (FPRL1), stimulates CCL2 production in human monocytes by activating extracellular-signal regulated kinase (ERK) and NF-kappaB. (PMID:18768891)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	saa	ENSDARG00000045999
drosophila_melanogaster	CG30467	FBGN0050467

Paralogs (3): SAA2 (ENSG00000134339), SAA4 (ENSG00000148965), SAAL1 (ENSG00000166788)

Protein

Protein identifiers

Serum amyloid A-1 protein — P0DJI8 (reviewed: P0DJI8)

All UniProt accessions (2): P0DJI8, A0A3B3ISW8

UniProt curated annotations — full annotation on UniProt →

Function. Major acute phase protein.

Subunit / interactions. Homohexamer; dimer of trimers. Can form amyloid fibrils after partial proteolysis; the native, undenatured protein does not form amyloid fibrils (in vitro). Apolipoprotein of the HDL complex. Binds to heparin.

Subcellular location. Secreted.

Tissue specificity. Expressed by the liver; secreted in plasma (at protein level).

Post-translational modifications. This protein is the precursor of amyloid protein A, which is formed by the removal of approximately 24 residues from the C-terminal end.

Disease relevance. Reactive, secondary amyloidosis is characterized by the extracellular accumulation in various tissues of the SAA1 protein. These deposits are highly insoluble and resistant to proteolysis; they disrupt tissue structure and compromise function. Elevated serum SAA1 protein levels may be associated with lung cancer.

Induction. Upon cytokine stimulation.

Polymorphism. At least 5 different SAA1 alleles have been described: SAA1.1 (SAA1alpha), SAA1.2 (SAA1beta), SAA1.3 (SAA1gamma), SAA1.4 (SAA1delta), SAA1.5 (also named SAA1beta but which differs from SAA1.2) (PubMed:10211414, PubMed:1546977, PubMed:1656519, PubMed:3839415, PubMed:8512321, PubMed:8670280, Ref.4). The sequence shown is that of SAA1.2.

Similarity. Belongs to the SAA family.

RefSeq proteins (3): NP_000322, NP_001171477, NP_954630* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000096	Serum_amyloid_A	Family
IPR052464	Synovial_Prolif_Regulator	Family

Pfam: PF00277

UniProt features (35 total): chain 7, sequence variant 7, mutagenesis site 6, helix 5, sequence conflict 4, region of interest 2, signal peptide 1, modified residue 1, strand 1, propeptide 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
4IP8	X-RAY DIFFRACTION	2.19
4IP9	X-RAY DIFFRACTION	2.5
7ZKY	ELECTRON MICROSCOPY	2.56
6MST	ELECTRON MICROSCOPY	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DJI8-F1	93.74	0.82

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 101

Mutagenesis-validated functional residues (6):

Position	Phenotype
19	reduces affinity for heparin and nearly abolishes association with hdl; when associated with a-80 and a-89.
33	reduces affinity for heparin; when associated with a-37 and a-65.
37	reduces affinity for heparin; when associated with a-33 and a-65.
65	reduces affinity for heparin; when associated with a-33 and a-37.
80	reduces affinity for heparin and nearly abolishes association with hdl; when associated with a-18 and a-89.
89	reduces affinity for heparin and nearly abolishes association with hdl; when associated with a-18 and a-80.

Function

Pathways and Gene Ontology

Reactome pathways

41 pathways

ID	Pathway
R-HSA-3000471	Scavenging by Class B Receptors
R-HSA-416476	G alpha (q) signalling events
R-HSA-418594	G alpha (i) signalling events
R-HSA-444473	Formyl peptide receptors bind formyl peptides and many other ligands
R-HSA-445989	TAK1-dependent IKK and NF-kappa-B activation
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling
R-HSA-879415	Advanced glycosylation endproduct receptor signaling
R-HSA-933542	TRAF6 mediated NF-kB activation
R-HSA-977225	Amyloid fiber formation
R-HSA-1280215	Cytokine Signaling in Immune system
R-HSA-162582	Signal Transduction
R-HSA-166016	Toll Like Receptor 4 (TLR4) Cascade
R-HSA-166058	MyD88:MAL(TIRAP) cascade initiated on plasma membrane
R-HSA-166166	MyD88-independent TLR4 cascade
R-HSA-168138	Toll Like Receptor 9 (TLR9) Cascade
R-HSA-168142	Toll Like Receptor 10 (TLR10) Cascade
R-HSA-168164	Toll Like Receptor 3 (TLR3) Cascade
R-HSA-168176	Toll Like Receptor 5 (TLR5) Cascade
R-HSA-168179	Toll Like Receptor TLR1:TLR2 Cascade
R-HSA-168181	Toll Like Receptor 7/8 (TLR7/8) Cascade
R-HSA-168188	Toll Like Receptor TLR6:TLR2 Cascade
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System
R-HSA-168898	Toll-like Receptor Cascades
R-HSA-168928	DDX58/IFIH1-mediated induction of interferon-alpha/beta
R-HSA-181438	Toll Like Receptor 2 (TLR2) Cascade
R-HSA-2173782	Binding and Uptake of Ligands by Scavenger Receptors
R-HSA-372790	Signaling by GPCR
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)
R-HSA-375276	Peptide ligand-binding receptors

MSigDB gene sets: 340 (showing top): REACTOME_DDX58_IFIH1_MEDIATED_INDUCTION_OF_INTERFERON_ALPHA_BETA, GSE45365_NK_CELL_VS_CD11B_DC_DN, MODULE_416, REACTOME_INNATE_IMMUNE_SYSTEM, MCLACHLAN_DENTAL_CARIES_UP, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_CELL_CHEMOTAXIS, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_INFLAMMATORY_RESPONSE, GOBP_PLATELET_ACTIVATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, KYNG_DNA_DAMAGE_DN, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, HUMMERICH_SKIN_CANCER_PROGRESSION_UP, GOBP_INTERLEUKIN_1_PRODUCTION

GO Biological Process (11): positive regulation of cytokine production (GO:0001819), acute-phase response (GO:0006953), positive regulation of cytosolic calcium ion concentration (GO:0007204), platelet activation (GO:0030168), neutrophil chemotaxis (GO:0030593), positive regulation of interleukin-1 production (GO:0032732), positive regulation of cell adhesion (GO:0045785), macrophage chemotaxis (GO:0048246), lymphocyte chemotaxis (GO:0048247), regulation of protein secretion (GO:0050708), negative regulation of inflammatory response (GO:0050728)

GO Molecular Function (2): G protein-coupled receptor binding (GO:0001664), heparin binding (GO:0008201)

GO Cellular Component (5): extracellular region (GO:0005576), cytoplasmic microtubule (GO:0005881), high-density lipoprotein particle (GO:0034364), extracellular exosome (GO:0070062), endocytic vesicle lumen (GO:0071682)

Reactome top-level categories

Rollup of top-19 pathways:

Category	Pathways
Toll-like Receptor Cascades	6
GPCR downstream signalling	2
Toll Like Receptor 4 (TLR4) Cascade	2
Binding and Uptake of Ligands by Scavenger Receptors	1
Peptide ligand-binding receptors	1
MyD88:MAL(TIRAP) cascade initiated on plasma membrane	1
Toll Like Receptor 3 (TLR3) Cascade	1
Interleukin-1 signaling	1
TRIF (TICAM1)-mediated TLR4 signaling	1
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation	1
MyD88 cascade initiated on plasma membrane	1
Signaling by Interleukins	1
Innate Immune System	1
DDX58/IFIH1-mediated induction of interferon-alpha/beta	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
leukocyte chemotaxis	2
cytokine production	1
regulation of cytokine production	1
positive regulation of gene expression	1
positive regulation of multicellular organismal process	1
acute inflammatory response	1
regulation of biological quality	1
cell activation	1
blood coagulation	1
granulocyte chemotaxis	1
neutrophil migration	1
positive regulation of cytokine production	1
interleukin-1 production	1
regulation of interleukin-1 production	1
cell adhesion	1
regulation of cell adhesion	1
positive regulation of cellular process	1
macrophage migration	1
lymphocyte migration	1
protein secretion	1
regulation of protein transport	1
regulation of secretion by cell	1
inflammatory response	1
negative regulation of defense response	1
negative regulation of response to external stimulus	1
regulation of inflammatory response	1
signaling receptor binding	1
glycosaminoglycan binding	1
sulfur compound binding	1
cellular anatomical structure	1
cytoplasm	1
microtubule	1
plasma lipoprotein particle	1
extracellular vesicle	1
endocytic vesicle	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SAA1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SAA1	SEMG1	psi-mi:“MI:0914”(association)	0.350

BioGRID (54): SAA1 (PCA), SAA1 (Reconstituted Complex), CACTIN (Affinity Capture-MS), PHF3 (Affinity Capture-MS), PRRC2A (Affinity Capture-MS), SAA2 (Affinity Capture-MS), YLPM1 (Affinity Capture-MS), ZC3H4 (Affinity Capture-MS), SLTM (Affinity Capture-MS), PPHLN1 (Affinity Capture-MS), NUDT12 (Affinity Capture-MS), DIDO1 (Affinity Capture-MS), SAFB (Affinity Capture-MS), EMC3 (Affinity Capture-MS), RAI14 (Affinity Capture-MS)

ESM2 similar proteins: B6HJA3, O56140, O89746, P02739, P02740, P04918, P05366, P05367, P09345, P09507, P0DJI8, P0DJI9, P0DSN9, P0DSO0, P11132, P11135, P18575, P19453, P19707, P19708, P19857, P20726, P20727, P22000, P35541, P35542, P35543, P42819, P53613, P53614, P81491, P87506, Q0CVD7, Q16625, Q2F4V2, Q32L76, Q6DEL2, Q6DPZ9, Q6DQ19, Q6DQ20

Diamond homologs: P02738, P02739, P02740, P04918, P05366, P05367, P0DJI8, P0DJI9, P0DSN9, P0DSO0, P18575, P19453, P19707, P19708, P19857, P20726, P20727, P22000, P31532, P35541, P35542, P35543, P42819, P53613, P53614, P81491, Q32L76, Q8SQ28

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	6
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

555 predictions. Top by Δscore:

Variant	Effect	Δscore
11:18269715:A:AG	acceptor_gain	1.0000
11:18269715:AGC:A	acceptor_gain	1.0000
11:18269716:G:GG	acceptor_gain	1.0000
11:18269716:GC:G	acceptor_gain	1.0000
11:18269716:GCG:G	acceptor_gain	1.0000
11:18269716:GCGAT:G	acceptor_gain	1.0000
11:18266294:CAGG:C	donor_loss	0.9900
11:18266295:AGGTG:A	donor_loss	0.9900
11:18266296:GGTGA:G	donor_loss	0.9900
11:18266297:G:GA	donor_loss	0.9900
11:18266298:T:A	donor_loss	0.9900
11:18269193:AGG:A	acceptor_gain	0.9900
11:18269194:GGG:G	acceptor_gain	0.9900
11:18269276:GGAAC:G	donor_gain	0.9900
11:18269277:G:T	donor_gain	0.9900
11:18269277:GAAC:G	donor_gain	0.9900
11:18269299:G:T	donor_gain	0.9900
11:18269329:ATCAC:A	donor_gain	0.9900
11:18269334:G:GG	donor_gain	0.9900
11:18269351:G:T	donor_gain	0.9900
11:18269708:T:A	acceptor_gain	0.9900
11:18269714:CAG:C	acceptor_loss	0.9900
11:18269716:G:GA	acceptor_loss	0.9900
11:18269716:GCGA:G	acceptor_gain	0.9900
11:18266882:A:AG	acceptor_gain	0.9800
11:18266883:G:GG	acceptor_gain	0.9800
11:18266883:GC:G	acceptor_gain	0.9800
11:18266883:GCACC:G	acceptor_gain	0.9800
11:18267060:G:GT	donor_gain	0.9800
11:18269193:AGGG:A	acceptor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001158505 (11:18264441 G>C), RS1002326844 (11:18264965 GAGGA>G), RS1002742689 (11:18268344 C>T), RS1003750316 (11:18266161 C>T), RS1004223370 (11:18265005 A>G,T), RS1004821246 (11:18267011 A>G), RS1004873583 (11:18266527 A>G), RS1005548302 (11:18270032 A>G), RS1005687760 (11:18264521 T>A), RS1007766898 (11:18269029 A>G), RS1008553224 (11:18265377 T>C), RS1009719660 (11:18265966 C>T), RS1009772151 (11:18265708 T>C), RS1011403833 (11:18268077 C>G), RS1011456720 (11:18267512 G>A)

Disease associations

OMIM: gene MIM:104750 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

32 total (30 of 32 shown, HPO-id order):

HPO	Term
HP:0000083	Renal insufficiency
HP:0000093	Proteinuria
HP:0000100	Nephrotic syndrome
HP:0000105	Enlarged kidney
HP:0000112	Nephropathy
HP:0000158	Macroglossia
HP:0000821	Hypothyroidism
HP:0000846	Adrenal insufficiency
HP:0000853	Goiter
HP:0001278	Orthostatic hypotension
HP:0001396	Cholestasis
HP:0001744	Splenomegaly
HP:0001917	Renal amyloidosis
HP:0001919	Acute kidney injury
HP:0002013	Vomiting
HP:0002018	Nausea
HP:0002024	Malabsorption
HP:0002027	Abdominal pain
HP:0002028	Chronic diarrhea
HP:0002240	Hepatomegaly
HP:0002615	Hypotension
HP:0004395	Malnutrition
HP:0004936	Venous thrombosis
HP:0005162	Abnormal left ventricular function
HP:0009830	Peripheral neuropathy
HP:0011034	Amyloid deposition
HP:0011830	Abnormal oral mucosa morphology
HP:0012185	Constrictive median neuropathy
HP:0012622	Chronic kidney disease
HP:0025077	Decreased QRS voltage

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST000876_3	Amyloid A serum levels	3.000000e-53
GCST005790_21	Rosacea symptom severity	5.000000e-06
GCST006585_398	Blood protein levels	8.000000e-248

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009180	rosacea severity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression, increases expression	4
Tobacco Smoke Pollution	affects expression, decreases expression	4
perfluorooctanoic acid	increases expression	2
tofacitinib	decreases reaction, increases expression	2
3’,4’-dimethoxy-alpha-naphthoflavone	decreases reaction, increases expression, affects cotreatment	2
Acetaminophen	decreases expression	2
Air Pollutants	increases abundance, increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Cisplatin	affects cotreatment, increases expression	2
Dexamethasone	increases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
baricitinib	decreases reaction, increases expression	1
2,2’,3,4’,5,5’,6-heptachlorobiphenyl	decreases expression	1
bisphenol F	decreases expression	1
perfluorodecanesulfonic acid	increases expression	1
parthenolide	decreases expression	1
propionaldehyde	increases expression	1
propylparaben	increases expression	1
bisphenol A	decreases expression	1
lead acetate	decreases expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
alpha-naphthoflavone	decreases reaction, increases expression	1
methylparaben	decreases expression, increases expression	1
sulforaphane	decreases expression	1
butyraldehyde	increases expression	1
cupric chloride	decreases expression	1
nickel sulfate	increases expression	1
transplatin	increases expression	1
deacylketoconazole	decreases expression	1
perfluorodecanoic acid	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1HD	Abcam A-549 SAA1 KO 2	Cancer cell line	Male
CVCL_B2PW	Abcam A-549 SAA1 KO 1	Cancer cell line	Male

Clinical trials (associated diseases)

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