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GeneBe

SAA1

serum amyloid A1, the group of Receptor ligands

Basic information

Region (hg38): 11:18266259-18269977

Previous symbols: [ "SAA" ]

Links

ENSG00000173432NCBI:6288OMIM:104750HGNC:10513Uniprot:P0DJI8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAA1 gene.

  • not provided (11 variants)
  • Inborn genetic diseases (6 variants)
  • Serum amyloid a variant (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAA1 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
1
clinvar
1
missense
7
clinvar
5
clinvar
2
clinvar
14
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 7 6 3

Variants in SAA1

This is a list of pathogenic ClinVar variants found in the SAA1 region.

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

Position Type Phenotype Significance ClinVar
11-18266966-G-A not specified Uncertain significance (Sep 20, 2023)3157450
11-18269190-T-G Benign (Dec 31, 2019)768433
11-18269272-C-T not specified Uncertain significance (Apr 12, 2022)2342073
11-18269273-G-A not specified Uncertain significance (Jan 26, 2022)2374146
11-18269285-A-T not specified Uncertain significance (Jan 16, 2024)3157448
11-18269302-C-T not specified Uncertain significance (Sep 12, 2023)2622360
11-18269312-C-T Benign/Likely benign (Apr 30, 2020)18108
11-18269319-T-C Likely benign (Dec 12, 2017)768434
11-18269325-A-C not specified Uncertain significance (Aug 17, 2022)2374445
11-18269327-T-C Benign (Apr 30, 2020)1258441
11-18269742-T-C Likely benign (Apr 16, 2018)717982
11-18269745-T-A Likely benign (Apr 16, 2018)717983
11-18269746-T-C Likely benign (Apr 16, 2018)718086
11-18269747-T-A Likely benign (Apr 16, 2018)718087
11-18269755-G-A Benign (Dec 31, 2019)18107
11-18269782-C-G not specified Uncertain significance (Oct 02, 2023)3157449
11-18269795-G-C not specified Uncertain significance (Aug 26, 2022)2309057
11-18269807-CAA-C Benign (Dec 31, 2019)787593
11-18269818-A-G Uncertain significance (Jul 01, 2022)2641661
11-18269827-G-C not specified Uncertain significance (Sep 14, 2022)2311610

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAA1protein_codingprotein_codingENST00000405158 33804
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01490.7041256900571257470.000227
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.01556868.40.9950.00000389783
Missense in Polyphen2323.1910.99178315
Synonymous-0.2562927.31.060.00000168232
Loss of Function0.64734.480.6703.41e-742

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001340.000123
Ashkenazi Jewish0.002930.00238
East Asian0.0001180.000109
Finnish0.000.00
European (Non-Finnish)0.0001330.000123
Middle Eastern0.0001180.000109
South Asian0.0004440.000425
Other0.0003870.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Major acute phase protein.;
Disease
DISEASE: Note=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. {ECO:0000269|PubMed:1463770}.; DISEASE: Note=Elevated serum SAA1 protein levels may be associated with lung cancer. {ECO:0000269|PubMed:1463770}.;
Pathway
Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;Interleukin-4 and 13 signaling;Signaling by GPCR;Toll Like Receptor 7/8 (TLR7/8) Cascade;Signal Transduction;Signaling by Interleukins;Vesicle-mediated transport;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;ZBP1(DAI) mediated induction of type I IFNs;Toll-Like Receptors Cascades;TRAF6 mediated NF-kB activation;DDX58/IFIH1-mediated induction of interferon-alpha/beta;DEx/H-box helicases activate type I IFN and inflammatory cytokines production ;Interleukin-1 signaling;Innate Immune System;Immune System;Formyl peptide receptors bind formyl peptides and many other ligands;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;RIP-mediated NFkB activation via ZBP1;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;G alpha (i) signalling events;Advanced glycosylation endproduct receptor signaling;Cytosolic sensors of pathogen-associated DNA ;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Scavenging by Class B Receptors;Binding and Uptake of Ligands by Scavenger Receptors;G alpha (q) signalling events;GPCR downstream signalling;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Endogenous TLR signaling;Interleukin-1 family signaling (Consensus)

Recessive Scores

pRec
0.518

Intolerance Scores

loftool
0.985
rvis_EVS
0.1
rvis_percentile_EVS
61.28

Haploinsufficiency Scores

pHI
0.0747
hipred
N
hipred_score
0.164
ghis
0.446

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.670

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Saa2
Phenotype
homeostasis/metabolism phenotype;

Gene ontology

Biological process
activation of MAPK activity;receptor-mediated endocytosis;acute-phase response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;cytokine-mediated signaling pathway;platelet activation;neutrophil chemotaxis;cellular protein metabolic process;innate immune response;positive regulation of cell adhesion;macrophage chemotaxis;lymphocyte chemotaxis;regulation of protein secretion;positive regulation of cytokine secretion;positive regulation of interleukin-1 secretion;negative regulation of inflammatory response;positive chemotaxis;cell chemotaxis
Cellular component
extracellular region;extracellular space;cytoplasmic microtubule;high-density lipoprotein particle;extracellular exosome;endocytic vesicle lumen
Molecular function
G protein-coupled receptor binding;heparin binding;chemoattractant activity