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GeneBe

S100A3

S100 calcium binding protein A3, the group of S100 calcium binding proteins

Basic information

Region (hg38): 1:153547328-153549258

Previous symbols: [ "S100E" ]

Links

ENSG00000188015NCBI:6274OMIM:176992HGNC:10493Uniprot:P33764AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A3 gene.

  • Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A3 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
3
clinvar
3
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 3 0 0

Variants in S100A3

This is a list of pathogenic ClinVar variants found in the S100A3 region.

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

Position Type Phenotype Significance ClinVar
1-153547718-G-C Inborn genetic diseases Uncertain significance (Jun 29, 2022)2299152
1-153547845-G-C Inborn genetic diseases Uncertain significance (Jan 10, 2022)2271715
1-153548449-C-A Inborn genetic diseases Uncertain significance (Jun 29, 2022)2341106
1-153548461-C-A Malignant tumor of prostate Uncertain significance (-)161603

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A3protein_codingprotein_codingENST00000368713 22044
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.007930.57212500337251257310.00290
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.07266159.41.030.00000348650
Missense in Polyphen1313.9050.93492173
Synonymous0.4682225.00.8810.00000150183
Loss of Function0.17233.340.8981.41e-741

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002690.00269
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.0005540.000554
European (Non-Finnish)0.005510.00552
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.002450.00245

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds both calcium and zinc. May be involved in calcium- dependent cuticle cell differentiation, hair shaft and hair cuticular barrier formation. {ECO:0000269|PubMed:18083705}.;

Recessive Scores

pRec
0.118

Intolerance Scores

loftool
0.715
rvis_EVS
0.61
rvis_percentile_EVS
83.07

Haploinsufficiency Scores

pHI
0.0946
hipred
N
hipred_score
0.170
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.911

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
S100a3
Phenotype

Gene ontology

Biological process
Cellular component
nucleolus;cytosol
Molecular function
calcium ion binding;zinc ion binding