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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:P06703AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • not specified (1 variants)
  • 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 S100A6 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 0
missense 1 1 2
nonsense 0
start loss 0
frameshift 1 1
inframe indel 0
splice variant 0
non coding 0
Total 0 0 2 0 1

Variants in S100A6

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

Position Type Phenotype Significance ClinVar
1-153534700-C-T Benign (Apr 24, 2018)link
1-153534779-T-C Inborn genetic diseases Uncertain significance (Jul 12, 2023)link
1-153534787-TC-T not specified Uncertain significance (Jan 06, 2020)link
1-153534817-G-A Inborn genetic diseases Uncertain significance (Jul 26, 2023)link
1-153535203-G-A Inborn genetic diseases Uncertain significance (Aug 15, 2023)link
1-153535279-C-T Inborn genetic diseases Uncertain significance (Feb 01, 2023)link
1-153535303-C-T Inborn genetic diseases Uncertain significance (Apr 21, 2022)link
1-153535336-C-A Inborn genetic diseases Uncertain significance (Apr 05, 2023)link

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