SAA1
serum amyloid A1, the group of Receptor ligands
Basic information
Region (hg38): 11:18266259-18269977
Previous symbols: [ "SAA" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (10 variants)
- Inborn genetic diseases (5 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 5 | 5 | 2 | 12 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 6 | 4 |
Variants in SAA1
This is a list of pathogenic ClinVar variants found in the SAA1 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-18269190-T-G | Benign (Dec 31, 2019) | |||
| 11-18269272-C-T | Inborn genetic diseases | Uncertain significance (Apr 12, 2022) | ||
| 11-18269273-G-A | Inborn genetic diseases | Uncertain significance (Jan 26, 2022) | ||
| 11-18269302-C-T | Inborn genetic diseases | Uncertain significance (Sep 12, 2023) | ||
| 11-18269312-C-T | Serum amyloid a variant | Benign/Likely benign (Apr 30, 2020) | ||
| 11-18269319-T-C | Likely benign (Dec 12, 2017) | |||
| 11-18269325-A-C | Inborn genetic diseases | Uncertain significance (Aug 17, 2022) | ||
| 11-18269327-T-C | Benign (Apr 30, 2020) | |||
| 11-18269742-T-C | Likely benign (Apr 16, 2018) | |||
| 11-18269745-T-A | Likely benign (Apr 16, 2018) | |||
| 11-18269746-T-C | Likely benign (Apr 16, 2018) | |||
| 11-18269747-T-A | Likely benign (Apr 16, 2018) | |||
| 11-18269755-G-A | Serum amyloid a variant | Benign (Dec 31, 2019) | ||
| 11-18269795-G-C | Inborn genetic diseases | Uncertain significance (Aug 26, 2022) | ||
| 11-18269807-CAA-C | Benign (Dec 31, 2019) | |||
| 11-18269818-A-G | Uncertain significance (Jul 01, 2022) | |||
| 11-18269827-G-C | Inborn genetic diseases | Uncertain significance (Sep 14, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SAA1 | protein_coding | protein_coding | ENST00000405158 | 3 | 3804 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0149 | 0.704 | 125690 | 0 | 57 | 125747 | 0.000227 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0155 | 68 | 68.4 | 0.995 | 0.00000389 | 783 |
| Missense in Polyphen | 23 | 23.191 | 0.99178 | 315 | ||
| Synonymous | -0.256 | 29 | 27.3 | 1.06 | 0.00000168 | 232 |
| Loss of Function | 0.647 | 3 | 4.48 | 0.670 | 3.41e-7 | 42 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000134 | 0.000123 |
| Ashkenazi Jewish | 0.00293 | 0.00238 |
| East Asian | 0.000118 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000133 | 0.000123 |
| Middle Eastern | 0.000118 | 0.000109 |
| South Asian | 0.000444 | 0.000425 |
| Other | 0.000387 | 0.000326 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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