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GeneBe

S100A11

S100 calcium binding protein A11, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:152032505-152047907

Links

ENSG00000163191NCBI:6282OMIM:603114HGNC:10488Uniprot:P31949AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A11 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 S100A11 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 S100A11

This is a list of pathogenic ClinVar variants found in the S100A11 region.

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

Position Type Phenotype Significance ClinVar
1-152032688-C-G Inborn genetic diseases Uncertain significance (Jul 26, 2021)2239316
1-152032745-C-T Inborn genetic diseases Uncertain significance (Apr 22, 2022)2284888
1-152032768-C-G Inborn genetic diseases Uncertain significance (May 05, 2022)2287634

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A11protein_codingprotein_codingENST00000271638 315402
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.008470.5861256950531257480.000211
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3095157.60.8850.00000292693
Missense in Polyphen711.6050.60317190
Synonymous0.5801821.40.8419.87e-7203
Loss of Function0.22533.450.8691.45e-745

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002230.00223
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00005310.0000527
Middle Eastern0.00005440.0000544
South Asian0.00006540.0000653
Other0.0003270.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Facilitates the differentiation and the cornification of keratinocytes. {ECO:0000269|PubMed:18618420}.;
Pathway
Neutrophil degranulation;Innate Immune System;Immune System;EGFR1 (Consensus)

Recessive Scores

pRec
0.198

Intolerance Scores

loftool
0.575
rvis_EVS
0.22
rvis_percentile_EVS
67.92

Haploinsufficiency Scores

pHI
0.143
hipred
Y
hipred_score
0.506
ghis
0.501

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
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
S100a11
Phenotype
reproductive system phenotype;

Gene ontology

Biological process
signal transduction;negative regulation of DNA replication;negative regulation of cell population proliferation;neutrophil degranulation;cell-cell adhesion
Cellular component
ruffle;extracellular region;extracellular space;nucleus;cytoplasm;cell-cell adherens junction;secretory granule lumen;extracellular exosome
Molecular function
calcium ion binding;protein binding;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding;cadherin binding involved in cell-cell adhesion