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GeneBe

S100A6

S100 calcium binding protein A6, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:153534598-153536244

Previous symbols: [ "CACY" ]

Links

ENSG00000197956NCBI:6277OMIM:114110HGNC:10496Uniprot:P06703AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A6 gene.

  • Inborn genetic diseases (6 variants)
  • not specified (1 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A6 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
6
clinvar
1
clinvar
7
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 7 0 1

Variants in S100A6

This is a list of pathogenic ClinVar variants found in the S100A6 region.

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

Position Type Phenotype Significance ClinVar
1-153534700-C-T Benign (Apr 24, 2018)777934
1-153534779-T-C not specified Uncertain significance (Jul 12, 2023)2593121
1-153534787-TC-T not specified Uncertain significance (Jan 06, 2020)1301708
1-153534817-G-A not specified Uncertain significance (Jul 26, 2023)2600986
1-153535203-G-A not specified Uncertain significance (Aug 15, 2023)2589747
1-153535279-C-T not specified Uncertain significance (Feb 01, 2023)2470525
1-153535303-C-T not specified Uncertain significance (Apr 21, 2022)2284603
1-153535336-C-A not specified Uncertain significance (Apr 05, 2023)2532433

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A6protein_codingprotein_codingENST00000368720 21646
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1760.656125734041257380.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2464347.80.9000.00000244587
Missense in Polyphen99.62260.9353136
Synonymous0.9151621.40.7480.00000108173
Loss of Function0.85312.440.4101.02e-734

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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 such as the reorganization of the actin cytoskeleton and in cell motility. Binds 2 calcium ions. Calcium binding is cooperative. {ECO:0000269|PubMed:22399290}.;
Pathway
Gastric Cancer Network 2;Vitamin D Receptor Pathway;Prostaglandin Synthesis and Regulation (Consensus)

Recessive Scores

pRec
0.586

Intolerance Scores

loftool
0.562
rvis_EVS
0.41
rvis_percentile_EVS
76.67

Haploinsufficiency Scores

pHI
0.152
hipred
Y
hipred_score
0.702
ghis
0.443

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.973

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
S100a6
Phenotype
homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype;

Gene ontology

Biological process
signal transduction;axonogenesis;ion transmembrane transport;positive regulation of fibroblast proliferation
Cellular component
ruffle;extracellular region;nucleus;nuclear envelope;cytoplasm;cytosol;plasma membrane;extrinsic component of cytoplasmic side of plasma membrane;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome
Molecular function
calcium ion binding;protein binding;tropomyosin binding;zinc ion binding;ion transmembrane transporter activity;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding