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S100A13

S100 calcium binding protein A13, the group of S100 calcium binding proteins

Basic information

Region (hg38): 1:153618786-153631360

Links

ENSG00000189171NCBI:6284OMIM:601989HGNC:10490Uniprot:Q99584AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A13 gene.

  • Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A13 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
0
missense
5
clinvar
1
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 1 0

Variants in S100A13

This is a list of pathogenic ClinVar variants found in the S100A13 region.

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

Position Type Phenotype Significance ClinVar
1-153618908-A-G not specified Uncertain significance (Jan 04, 2024)3157387
1-153618950-CCAAT-C Uncertain significance (Mar 26, 2024)3065489
1-153618971-T-C not specified Uncertain significance (May 06, 2022)2373967
1-153618986-G-A not specified Uncertain significance (Sep 28, 2022)2361785
1-153618994-A-T not specified Uncertain significance (Dec 01, 2022)2406058
1-153626370-C-T not specified Likely benign (Aug 02, 2022)2398287
1-153626390-C-T not specified Uncertain significance (Nov 08, 2022)2324790
1-153626420-G-A not specified Uncertain significance (Dec 19, 2023)3157388
1-153626453-G-A not specified Uncertain significance (Nov 12, 2021)2260489
1-153630581-G-A Benign (Jun 12, 2018)725490
1-153630640-C-T not specified Uncertain significance (Jun 12, 2023)2515898

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A13protein_codingprotein_codingENST00000368699 215306
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04970.7031257270161257430.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3154652.40.8770.00000270649
Missense in Polyphen915.90.56602206
Synonymous0.4652022.80.8760.00000134180
Loss of Function0.65623.280.6091.38e-742

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008790.00000879
Middle Eastern0.000.00
South Asian0.0004570.000457
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in the export of proteins that lack a signal peptide and are secreted by an alternative pathway. Binds two calcium ions per subunit. Binds one copper ion. Binding of one copper ion does not interfere with calcium binding. Required for the copper-dependent stress-induced export of IL1A and FGF1. The calcium-free protein binds to lipid vesicles containing phosphatidylserine, but not to vesicles containing phosphatidylcholine (By similarity). {ECO:0000250, ECO:0000269|PubMed:12746488, ECO:0000269|PubMed:20863990}.;

Intolerance Scores

loftool
0.817
rvis_EVS
0.17
rvis_percentile_EVS
65.33

Haploinsufficiency Scores

pHI
0.118
hipred
N
hipred_score
0.245
ghis
0.500

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.978

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
S100a13
Phenotype

Gene ontology

Biological process
positive regulation of cell population proliferation;regulation of cell shape;positive regulation of I-kappaB kinase/NF-kappaB signaling;mast cell degranulation;response to copper ion;cytokine secretion;interleukin-1 alpha secretion;response to electrical stimulus
Cellular component
extracellular region;extracellular space;nucleus;nucleolus;cytoplasm;cytosol;plasma membrane;mast cell granule;perinuclear region of cytoplasm
Molecular function
copper ion binding;calcium ion binding;protein binding;zinc ion binding;lipid binding;fibroblast growth factor binding;protein homodimerization activity;RAGE receptor binding