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GeneBe

S100A10

S100 calcium binding protein A10, the group of S100 calcium binding proteins

Basic information

Region (hg38): 1:151982914-151993859

Previous symbols: [ "ANX2LG", "CAL1L" ]

Links

ENSG00000197747NCBI:6281OMIM:114085HGNC:10487Uniprot:P60903AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A10 gene.

  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A10 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
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 0 0

Variants in S100A10

This is a list of pathogenic ClinVar variants found in the S100A10 region.

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

Position Type Phenotype Significance ClinVar
1-151986178-T-G Inborn genetic diseases Uncertain significance (Mar 25, 2022)2279883

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A10protein_codingprotein_codingENST00000368811 211476
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1680.654116709011167100.00000428
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6833548.40.7240.00000221657
Missense in Polyphen04.125078
Synonymous-0.1261817.31.049.87e-7157
Loss of Function0.80812.330.4299.59e-839

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006510.0000651
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Because S100A10 induces the dimerization of ANXA2/p36, it may function as a regulator of protein phosphorylation in that the ANXA2 monomer is the preferred target (in vitro) of tyrosine- specific kinase.;
Pathway
Prostaglandin Synthesis and Regulation;Dissolution of Fibrin Clot;EGFR1;Hemostasis (Consensus)

Recessive Scores

pRec
0.292

Intolerance Scores

loftool
0.385
rvis_EVS
0.13
rvis_percentile_EVS
62.74

Haploinsufficiency Scores

pHI
0.552
hipred
Y
hipred_score
0.506
ghis
0.478

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.991

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumLowMedium

Mouse Genome Informatics

Gene name
S100a10
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process
membrane raft assembly;vesicle budding from membrane;positive regulation of GTPase activity;positive regulation of binding;protein heterotetramerization;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;protein localization to plasma membrane;positive regulation of substrate adhesion-dependent cell spreading
Cellular component
extracellular region;extrinsic component of plasma membrane;membrane raft;collagen-containing extracellular matrix;extracellular exosome
Molecular function
calcium ion binding;protein binding;lipid binding;protein homodimerization activity;ion channel binding