S100A12 (S100 calcium binding protein A12) - Rat Genome Database

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Gene: S100A12 (S100 calcium binding protein A12) Homo sapiens
Analyze
Symbol: S100A12
Name: S100 calcium binding protein A12
RGD ID: 1352115
HGNC Page HGNC:10489
Description: Enables RAGE receptor binding activity and identical protein binding activity. Involved in defense response to other organism; positive regulation of canonical NF-kappaB signal transduction; and xenobiotic metabolic process. Located in cytoplasm and nucleus.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: CAAF1; CAGC; calcitermin; calcium-binding protein in amniotic fluid 1; calgranulin C; calgranulin-C; CGRP; EN-RAGE; ENRAGE; extracellular newly identified RAGE-binding protein; migration inhibitory factor-related protein 6; MRP-6; MRP6; neutrophil S100 protein; p6; protein S100-A12; s100 calcium binding protein a12 (calgranulin c); S100 calcium-binding protein A12 (calgranulin C)
RGD Orthologs
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381153,373,711 - 153,375,621 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1153,373,711 - 153,375,621 (-)EnsemblGRCh38hg38GRCh38
GRCh371153,346,187 - 153,348,097 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,612,808 - 151,614,699 (-)NCBINCBI36Build 36hg18NCBI36
Build 341150,159,256 - 150,161,148NCBI
Celera1126,417,439 - 126,419,330 (-)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,709,595 - 124,711,486 (-)NCBIHuRef
CHM1_11154,741,897 - 154,743,788 (-)NCBICHM1_1
T2T-CHM13v2.01152,510,935 - 152,512,845 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IDA,IEA)
cytoskeleton  (IEA,TAS)
cytosol  (TAS)
extracellular region  (IEA,TAS)
nucleus  (IDA)
plasma membrane  (IEA,TAS)
secretory granule lumen  (TAS)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7626002   PMID:7759097   PMID:8619860   PMID:8619876   PMID:8769108   PMID:8985590   PMID:10399917   PMID:10531386   PMID:10666601   PMID:11134923   PMID:11522286   PMID:11856825  
PMID:11884208   PMID:11884210   PMID:12042313   PMID:12218151   PMID:12477932   PMID:12697438   PMID:12699958   PMID:12740341   PMID:12777802   PMID:15033494   PMID:15077313   PMID:15489334  
PMID:16253391   PMID:16710414   PMID:16804393   PMID:16864903   PMID:17158877   PMID:17328050   PMID:17787039   PMID:17852869   PMID:18029348   PMID:18050248   PMID:18257809   PMID:18292089  
PMID:18346834   PMID:18443896   PMID:18663285   PMID:19201044   PMID:19284577   PMID:19386136   PMID:19501594   PMID:19530996   PMID:19542470   PMID:19576587   PMID:19875725   PMID:20025991  
PMID:20437698   PMID:20461025   PMID:20512925   PMID:20537326   PMID:20847094   PMID:20966394   PMID:21067798   PMID:21258041   PMID:21418345   PMID:21724696   PMID:21822023   PMID:21873635  
PMID:21906738   PMID:22549347   PMID:22609404   PMID:22786469   PMID:22796048   PMID:22818064   PMID:23171632   PMID:23324110   PMID:23377171   PMID:23398829   PMID:23609464   PMID:23921255  
PMID:23942785   PMID:24307989   PMID:24341566   PMID:24378957   PMID:24622086   PMID:24691129   PMID:24887223   PMID:24944024   PMID:24975020   PMID:25282581   PMID:25302747   PMID:25313445  
PMID:25341801   PMID:25438075   PMID:25625487   PMID:25650963   PMID:25825217   PMID:25854354   PMID:25964473   PMID:26274928   PMID:26333514   PMID:26339162   PMID:26638166   PMID:26767827  
PMID:26914918   PMID:27057553   PMID:27355424   PMID:27539060   PMID:27598566   PMID:27689623   PMID:27734162   PMID:27840235   PMID:28110121   PMID:28125622   PMID:28381820   PMID:28735301  
PMID:28756107   PMID:28816402   PMID:28834384   PMID:28964306   PMID:29080693   PMID:29902210   PMID:29906464   PMID:29943619   PMID:29944393   PMID:30235276   PMID:30406853   PMID:30426025  
PMID:30447136   PMID:30563403   PMID:30594066   PMID:30957488   PMID:31035738   PMID:31199706   PMID:31666644   PMID:31818258   PMID:31865833   PMID:32015423   PMID:32082330   PMID:32228516  
PMID:32513696   PMID:32514673   PMID:32582175   PMID:32723832   PMID:33068321   PMID:33259383   PMID:33469045   PMID:33576586   PMID:34108608   PMID:34514516   PMID:34745092   PMID:35016442  
PMID:35140322   PMID:35938962   PMID:36555597   PMID:36637406   PMID:37863883   PMID:37880318   PMID:38492210  


Genomics

Comparative Map Data
S100A12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381153,373,711 - 153,375,621 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1153,373,711 - 153,375,621 (-)EnsemblGRCh38hg38GRCh38
GRCh371153,346,187 - 153,348,097 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,612,808 - 151,614,699 (-)NCBINCBI36Build 36hg18NCBI36
Build 341150,159,256 - 150,161,148NCBI
Celera1126,417,439 - 126,419,330 (-)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,709,595 - 124,711,486 (-)NCBIHuRef
CHM1_11154,741,897 - 154,743,788 (-)NCBICHM1_1
T2T-CHM13v2.01152,510,935 - 152,512,845 (-)NCBIT2T-CHM13v2.0
S100A12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2196,462,114 - 96,464,031 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1196,197,768 - 96,199,685 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01128,725,102 - 128,727,021 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11132,354,132 - 132,356,085 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1132,354,132 - 132,356,085 (-)Ensemblpanpan1.1panPan2
S100A12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1743,554,078 - 43,555,470 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl743,554,146 - 43,555,475 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha743,046,910 - 43,048,352 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0743,503,704 - 43,505,146 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl743,503,822 - 43,505,151 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1743,206,024 - 43,207,465 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0743,259,932 - 43,261,373 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0743,543,469 - 43,544,911 (+)NCBIUU_Cfam_GSD_1.0
S100A12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl496,225,691 - 96,227,127 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1496,225,691 - 96,227,030 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24105,075,389 - 105,076,728 (-)NCBISscrofa10.2Sscrofa10.2susScr3
S100A12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12010,377,418 - 10,379,638 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660389,847,458 - 9,848,394 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in S100A12
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q21.3(chr1:152951169-153495655)x3 copy number gain See cases [RCV000136561] Chr1:152951169..153495655 [GRCh38]
Chr1:152923645..153468131 [GRCh37]
Chr1:151190269..151734755 [NCBI36]
Chr1:1q21.3		 uncertain significance
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q21.3(chr1:150853044-154647786)x3 copy number gain not provided [RCV000684655] Chr1:150853044..154647786 [GRCh37]
Chr1:1q21.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NM_005621.2(S100A12):c.18G>A (p.Glu6=) single nucleotide variant not provided [RCV000949651] Chr1:153374575 [GRCh38]
Chr1:153347051 [GRCh37]
Chr1:1q21.3		 benign
GRCh37/hg19 1q21.3(chr1:153321482-153835605)x3 copy number gain not provided [RCV000847221] Chr1:153321482..153835605 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q21.3(chr1:153061323-153904594)x3 copy number gain not provided [RCV001005141] Chr1:153061323..153904594 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q21.3(chr1:153007105-153463223)x3 copy number gain not provided [RCV001258470] Chr1:153007105..153463223 [GRCh37]
Chr1:1q21.3		 uncertain significance
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NC_000001.10:g.(?_149895434)_(156851434_?)dup duplication Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency [RCV001958273]|Congenital neutropenia-myelofibrosis-nephromegaly syndrome [RCV001958271]|Kostmann syndrome [RCV003120769]|MHC class II deficiency [RCV001992607] Chr1:149895434..156851434 [GRCh37]
Chr1:1q21.2-23.1		 uncertain significance
NM_005621.2(S100A12):c.133A>G (p.Ile45Val) single nucleotide variant not specified [RCV004160874] Chr1:153374460 [GRCh38]
Chr1:153346936 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_005621.2(S100A12):c.161T>A (p.Ile54Asn) single nucleotide variant not specified [RCV004126476] Chr1:153373945 [GRCh38]
Chr1:153346421 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_005621.2(S100A12):c.19C>A (p.His7Asn) single nucleotide variant not specified [RCV004133403] Chr1:153374574 [GRCh38]
Chr1:153347050 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_005621.2(S100A12):c.56C>T (p.Ser19Leu) single nucleotide variant not specified [RCV004107208] Chr1:153374537 [GRCh38]
Chr1:153347013 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_005621.2(S100A12):c.208G>T (p.Asp70Tyr) single nucleotide variant not specified [RCV004176533] Chr1:153373898 [GRCh38]
Chr1:153346374 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_005621.2(S100A12):c.196G>T (p.Asp66Tyr) single nucleotide variant not specified [RCV004095717] Chr1:153373910 [GRCh38]
Chr1:153346386 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q12-23.1(chr1:142535935-157648813)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV003329522] Chr1:142535935..157648813 [GRCh37]
Chr1:1q12-23.1		 pathogenic
GRCh37/hg19 1q21.3(chr1:153097950-153481118)x3 copy number gain not provided [RCV003484039] Chr1:153097950..153481118 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 copy number gain not specified [RCV003986717] Chr1:144368497..158992086 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:146577511-157155587)x3 copy number gain not specified [RCV003987261] Chr1:146577511..157155587 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
NM_005621.2(S100A12):c.154G>T (p.Ala52Ser) single nucleotide variant not specified [RCV004447228] Chr1:153373952 [GRCh38]
Chr1:153346428 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_005621.2(S100A12):c.242C>A (p.Ala81Glu) single nucleotide variant not specified [RCV004447229] Chr1:153373864 [GRCh38]
Chr1:153346340 [GRCh37]
Chr1:1q21.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:176
Interacting mature miRNAs:178
Transcripts:ENST00000368737
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
G54103  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371153,346,227 - 153,346,361UniSTSGRCh37
Build 361151,612,851 - 151,612,985RGDNCBI36
Celera1126,417,482 - 126,417,616RGD
Cytogenetic Map1q21UniSTS
HuRef1124,709,638 - 124,709,772UniSTS
WI-17060  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371153,346,203 - 153,346,352UniSTSGRCh37
Build 361151,612,827 - 151,612,976RGDNCBI36
Celera1126,417,458 - 126,417,607RGD
Cytogenetic Map1q21UniSTS
HuRef1124,709,614 - 124,709,763UniSTS
GeneMap99-GB4 RH Map1551.46UniSTS
GeneMap99-GB4 RH Map1552.71UniSTS
Whitehead-RH Map1652.1UniSTS
NCBI RH Map11248.3UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component
High 527 568 3 18
Medium 230 607 280 113 482 78 276 172 252 51 204 711 38 467 117 1
Low 1601 1571 1195 381 242 278 2734 1583 2548 267 884 626 106 705 1904 1
Below cutoff 395 200 165 75 78 60 778 307 661 54 226 66 21 1 25 560 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000368737   ⟹   ENSP00000357726
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1153,373,711 - 153,375,621 (-)Ensembl
RefSeq Acc Id: NM_005621   ⟹   NP_005612
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381153,373,711 - 153,375,621 (-)NCBI
GRCh371153,346,184 - 153,348,075 (-)ENTREZGENE
Build 361151,612,808 - 151,614,699 (-)NCBI Archive
HuRef1124,709,595 - 124,711,486 (-)ENTREZGENE
CHM1_11154,741,897 - 154,743,788 (-)NCBI
T2T-CHM13v2.01152,510,935 - 152,512,845 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_005612   ⟸   NM_005621
- UniProtKB: Q5SY66 (UniProtKB/Swiss-Prot),   P83219 (UniProtKB/Swiss-Prot),   Q7M4R1 (UniProtKB/Swiss-Prot),   P80511 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000357726   ⟸   ENST00000368737
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P80511-F1-model_v2 AlphaFold P80511 1-92 view protein structure

Promoters
RGD ID:6857190
Promoter ID:EPDNEW_H1760
Type:initiation region
Name:S100A12_1
Description:S100 calcium binding protein A12
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381153,375,598 - 153,375,658EPDNEW

Additional Information

Database Acc Id Source(s)
COSMIC S100A12 COSMIC
Ensembl Genes ENSG00000163221 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000368737 ENTREZGENE
  ENST00000368737.5 UniProtKB/Swiss-Prot
Gene3D-CATH EF-hand UniProtKB/Swiss-Prot
GTEx ENSG00000163221 GTEx
HGNC ID HGNC:10489 ENTREZGENE
Human Proteome Map S100A12 Human Proteome Map
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  S100/CaBP-9k_CS UniProtKB/Swiss-Prot
  S100_Ca-bd_sub UniProtKB/Swiss-Prot
KEGG Report hsa:6283 UniProtKB/Swiss-Prot
NCBI Gene 6283 ENTREZGENE
OMIM 603112 OMIM
PANTHER PROTEIN S100-A12 UniProtKB/Swiss-Prot
  S100 CALCIUM-BINDING PROTEIN UniProtKB/Swiss-Prot
Pfam S_100 UniProtKB/Swiss-Prot
PharmGKB PA34901 PharmGKB, RGD
PROSITE EF_HAND_2 UniProtKB/Swiss-Prot
  S100_CABP UniProtKB/Swiss-Prot
SMART S_100 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
UniProt P80511 ENTREZGENE
  P83219 ENTREZGENE
  Q5SY66 ENTREZGENE
  Q7M4R1 ENTREZGENE
  S10AC_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary P83219 UniProtKB/Swiss-Prot
  Q5SY66 UniProtKB/Swiss-Prot
  Q7M4R1 UniProtKB/Swiss-Prot