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GeneBe

S100A2

S100 calcium binding protein A2, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:153561107-153567890

Previous symbols: [ "S100L" ]

Links

ENSG00000196754NCBI:6273OMIM:176993HGNC:10492Uniprot:P29034AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A2 gene.

  • not provided (1 variants)
  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A2 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
clinvar
2
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 1

Variants in S100A2

This is a list of pathogenic ClinVar variants found in the S100A2 region.

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

Position Type Phenotype Significance ClinVar
1-153563852-G-A not specified Uncertain significance (Jun 06, 2023)2557212
1-153563870-C-G Benign (Jul 05, 2018)778812

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A2protein_codingprotein_codingENST00000368708 26783
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00005840.1561256720631257350.000251
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.03874949.80.9850.00000231645
Missense in Polyphen1814.1231.2745196
Synonymous-0.4282421.51.120.00000111175
Loss of Function-1.4752.502.001.05e-736

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008090.000809
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00009240.0000924
European (Non-Finnish)0.0001760.000176
Middle Eastern0.000.00
South Asian0.0002940.000294
Other0.0006520.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: May function as calcium sensor and modulator, contributing to cellular calcium signaling. May function by interacting with other proteins, such as TPR-containing proteins, and indirectly play a role in many physiological processes. May also play a role in suppressing tumor cell growth. {ECO:0000269|PubMed:1372446, ECO:0000269|PubMed:22399290}.;
Pathway
Vitamin D Receptor Pathway;p73 transcription factor network;Validated transcriptional targets of TAp63 isoforms;Direct p53 effectors (Consensus)

Recessive Scores

pRec
0.203

Intolerance Scores

loftool
0.674
rvis_EVS
0.17
rvis_percentile_EVS
65.33

Haploinsufficiency Scores

pHI
0.153
hipred
N
hipred_score
0.461
ghis
0.423

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.601

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
endothelial cell migration
Cellular component
cellular_component
Molecular function
calcium ion binding;protein binding;identical protein binding;transition metal ion binding