S100A12

S100 calcium binding protein A12, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153373710-153375621

Links

ENSG00000163221 ∙ NCBI:6283 ∙ OMIM:603112 ∙ HGNC:10489 ∙ Uniprot:P80511 ∙ 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 S100A12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A12 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in S100A12

This is a list of pathogenic ClinVar variants found in the S100A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153373864-G-T		not specified	Uncertain significance (Nov 29, 2023)
1-153373898-C-A		not specified	Uncertain significance (Nov 21, 2022)
1-153373910-C-A		not specified	Uncertain significance (Jun 11, 2021)
1-153373945-A-T		not specified	Uncertain significance (Jan 31, 2022)
1-153373952-C-A		not specified	Uncertain significance (Dec 12, 2023)
1-153374460-T-C		not specified	Uncertain significance (Sep 27, 2022)
1-153374537-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-153374574-G-T		not specified	Uncertain significance (Mar 16, 2022)
1-153374575-C-T			Benign (Jan 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A12	protein_coding	protein_coding	ENST00000368737	2	1942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.482	0.443	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.580	60	48.6	1.23	0.00000235	611
Missense in Polyphen		20	12.774	1.5657		190
Synonymous	-1.28	27	19.7	1.37	0.00000100	174
Loss of Function	1.24	0	1.78	0.00	7.45e-8	23

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: S100A12 is a calcium-, zinc- and copper-binding protein which plays a prominent role in the regulation of inflammatory processes and immune response. Its proinflammatory activity involves 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 receptor for advanced glycation endproducts (AGER). Binding to AGER activates the MAP-kinase and NF-kappa-B signaling pathways leading to production of proinflammatory cytokines and up-regulation of cell adhesion molecules ICAM1 and VCAM1. Acts as a monocyte and mast cell chemoattractant. Can stimulate mast cell degranulation and activation which generates chemokines, histamine and cytokines inducing further leukocyte recruitment to the sites of inflammation. Can inhibit the activity of matrix metalloproteinases; MMP2, MMP3 and MMP9 by chelating Zn(2+) from their active sites. Possesses filariacidal and filariastatic activity. Calcitermin possesses antifungal activity against C.albicans and is also active against E.coli and P.aeruginosa but not L.monocytogenes and S.aureus. {ECO:0000269|PubMed:11522286, ECO:0000269|PubMed:17208591, ECO:0000269|PubMed:18292089, ECO:0000269|PubMed:19386136}.
• Pathway: Toll Like Receptor 7/8 (TLR7/8) Cascade;Neutrophil degranulation;Signaling by Interleukins;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;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;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;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;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.450
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.0141
• hipred: N
• hipred_score: 0.123
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00651

Gene Damage Prediction

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

Gene ontology

• Biological process: monocyte chemotaxis;xenobiotic metabolic process;inflammatory response;neutrophil chemotaxis;killing of cells of other organism;defense response to bacterium;positive regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;positive regulation of MAP kinase activity;innate immune response;mast cell activation;cytokine secretion;positive regulation of inflammatory response;defense response to fungus;positive regulation of NF-kappaB transcription factor activity;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular region;nucleus;cytoplasm;cytosol;cytoskeleton;plasma membrane;secretory granule lumen
• Molecular function: copper ion binding;calcium ion binding;protein binding;zinc ion binding;RAGE receptor binding