S100A9

S100 calcium binding protein A9, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153357853-153361023

Previous symbols: [ "CAGB", "CFAG" ]

Links

ENSG00000163220 ∙ NCBI:6280 ∙ OMIM:123886 ∙ HGNC:10499 ∙ Uniprot:P06702 ∙ 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 S100A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A9 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				3		3
missense			3	2	1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	3	5	1

Variants in S100A9

This is a list of pathogenic ClinVar variants found in the S100A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153358287-A-T		not specified	Likely benign (Jul 25, 2023)
1-153358312-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-153358315-A-G		not specified	Likely benign (Jan 17, 2023)
1-153358388-G-A			Likely benign (Jun 27, 2018)
1-153360639-C-T			Benign (May 24, 2018)
1-153360700-T-C			Likely benign (May 15, 2018)
1-153360728-T-C		not specified	Uncertain significance (Feb 01, 2023)
1-153360781-G-A			Likely benign (Jul 18, 2018)
1-153360788-G-A			Benign (Jul 21, 2018)
1-153360827-G-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A9	protein_coding	protein_coding	ENST00000368738	2	3174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.478	0.445	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.575	50	62.8	0.796	0.00000325	768
Missense in Polyphen		12	16.623	0.72188		226
Synonymous	-0.692	31	26.5	1.17	0.00000163	202
Loss of Function	1.22	0	1.74	0.00	7.35e-8	22

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S100A9 is a calcium- and zinc-binding protein which plays a prominent role in the regulation of inflammatory processes and immune response. It can induce neutrophil chemotaxis, adhesion, can increase the bactericidal activity of neutrophils by promoting phagocytosis via activation of SYK, PI3K/AKT, and ERK1/2 and can induce degranulation of neutrophils by a MAPK-dependent mechanism. Predominantly found as calprotectin (S100A8/A9) which has a wide plethora of intra- and extracellular functions. The intracellular functions include: facilitating leukocyte arachidonic acid trafficking and metabolism, modulation of the tubulin-dependent cytoskeleton during migration of phagocytes and activation of the neutrophilic NADPH-oxidase. Activates NADPH- oxidase by facilitating the enzyme complex assembly at the cell membrane, transferring arachidonic acid, an essential cofactor, to the enzyme complex and S100A8 contributes to the enzyme assembly by directly binding to NCF2/P67PHOX. The extracellular functions involve proinflammatory, antimicrobial, oxidant-scavenging and apoptosis-inducing activities. Its proinflammatory activity includes recruitment of leukocytes, promotion of cytokine and chemokine production, and regulation of leukocyte adhesion and migration. Acts as an alarmin or a danger associated molecular pattern (DAMP) molecule and stimulates innate immune cells via binding to pattern recognition receptors such as Toll-like receptor 4 (TLR4) and receptor for advanced glycation endproducts (AGER). Binding to TLR4 and AGER activates the MAP-kinase and NF- kappa-B signaling pathways resulting in the amplification of the proinflammatory cascade. Has antimicrobial activity towards bacteria and fungi and exerts its antimicrobial activity probably via chelation of Zn(2+) which is essential for microbial growth. Can induce cell death via autophagy and apoptosis and this occurs through the cross-talk of mitochondria and lysosomes via reactive oxygen species (ROS) and the process involves BNIP3. Can regulate neutrophil number and apoptosis by an anti-apoptotic effect; regulates cell survival via ITGAM/ITGB and TLR4 and a signaling mechanism involving MEK-ERK. Its role as an oxidant scavenger has a protective role in preventing exaggerated tissue damage by scavenging oxidants. Can act as a potent amplifier of inflammation in autoimmunity as well as in cancer development and tumor spread. Has transnitrosylase activity; in oxidatively-modified low- densitity lipoprotein (LDL(ox))-induced S-nitrosylation of GAPDH on 'Cys-247' proposed to transfer the NO moiety from NOS2/iNOS to GAPDH via its own S-nitrosylated Cys-3. The iNOS-S100A8/A9 transnitrosylase complex is proposed to also direct selective inflammatory stimulus-dependent S-nitrosylation of multiple targets such as ANXA5, EZR, MSN and VIM by recognizing a [IL]-x-C- x-x-[DE] motif. {ECO:0000269|PubMed:12626582, ECO:0000269|PubMed:15331440, ECO:0000269|PubMed:15598812, ECO:0000269|PubMed:15642721, ECO:0000269|PubMed:16258195, ECO:0000269|PubMed:19087201, ECO:0000269|PubMed:19122197, ECO:0000269|PubMed:19402754, ECO:0000269|PubMed:19534726, ECO:0000269|PubMed:19935772, ECO:0000269|PubMed:20103766, ECO:0000269|PubMed:21325622, ECO:0000269|PubMed:21487906, ECO:0000269|PubMed:22363402, ECO:0000269|PubMed:22804476, ECO:0000269|PubMed:22808130, ECO:0000269|PubMed:25417112, ECO:0000269|PubMed:8423249}.
• Pathway: IL-17 signaling pathway - Homo sapiens (human);IL1 and megakaryocytes in obesity;Vitamin D Receptor Pathway;Neutrophil degranulation;Toll-Like Receptors Cascades;Antimicrobial peptides;Innate Immune System;Immune System;Regulation of TLR by endogenous ligand;Endogenous TLR signaling;Metal sequestration by antimicrobial proteins (Consensus)

Recessive Scores

• pRec: 0.451

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.436
• hipred: N
• hipred_score: 0.418
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: S100a9
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: cytokine production;toll-like receptor signaling pathway;leukocyte migration involved in inflammatory response;autophagy;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;inflammatory response;cell-cell signaling;positive regulation of neuron projection development;antimicrobial humoral response;positive regulation of cell growth;neutrophil chemotaxis;sequestering of zinc ion;chemokine production;peptidyl-cysteine S-trans-nitrosylation;modification of morphology or physiology of other organism;defense response to bacterium;neutrophil degranulation;innate immune response;positive regulation of inflammatory response;defense response to fungus;positive regulation of NF-kappaB transcription factor activity;regulation of cytoskeleton organization;antimicrobial humoral immune response mediated by antimicrobial peptide;neutrophil aggregation;cellular oxidant detoxification;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: extracellular region;extracellular space;nucleus;nucleoplasm;cytoplasm;cytosol;cytoskeleton;plasma membrane;cell junction;secretory granule lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: calcium ion binding;protein binding;microtubule binding;zinc ion binding;antioxidant activity;Toll-like receptor 4 binding;arachidonic acid binding;RAGE receptor binding