SAA1

serum amyloid A1, the group of Receptor ligands

Basic information

Region (hg38): 11:18266260-18269977

Previous symbols: [ "SAA" ]

Links

ENSG00000173432 ∙ NCBI:6288 ∙ OMIM:104750 ∙ HGNC:10513 ∙ Uniprot:P0DJI8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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		1
missense			10	5	2	17
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	10	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)
11-18269190-T-G			Benign (Dec 31, 2019)
11-18269272-C-T		not specified	Uncertain significance (Apr 12, 2022)
11-18269273-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-18269285-A-T		not specified	Uncertain significance (Jan 16, 2024)
11-18269302-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-18269312-C-T			Benign/Likely benign (Apr 30, 2020)
11-18269319-T-C			Likely benign (Dec 12, 2017)
11-18269325-A-C		not specified	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			Benign (Dec 31, 2019)
11-18269782-C-G		not specified	Uncertain significance (Oct 02, 2023)
11-18269795-G-C		not specified	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		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

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: 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_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