Menu
GeneBe

S100A1

S100 calcium binding protein A1, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153627925-153632039

Previous symbols: [ "S100A" ]

Links

ENSG00000160678NCBI:6271OMIM:176940HGNC:10486Uniprot:P23297AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A1 gene.

  • Inborn genetic diseases (3 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A1 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
1
clinvar
1
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 1

Variants in S100A1

This is a list of pathogenic ClinVar variants found in the S100A1 region.

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

Position Type Phenotype Significance ClinVar
1-153630581-G-A Benign (Jun 12, 2018)725490
1-153630640-C-T not specified Uncertain significance (Jun 12, 2023)2515898
1-153631727-G-T not specified Uncertain significance (Nov 22, 2022)2329285
1-153631798-C-T not specified Uncertain significance (Sep 17, 2021)2352245
1-153631835-C-G not specified Uncertain significance (Dec 27, 2023)3157381

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A1protein_codingprotein_codingENST00000292169 24112
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.006000.513125739081257470.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1555753.81.060.00000296624
Missense in Polyphen2418.6991.2835231
Synonymous-0.1332726.11.030.00000185174
Loss of Function-0.061532.891.041.20e-741

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009050.0000904
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probably acts as a Ca(2+) signal transducer (PubMed:22399290). In response to an increase in intracellular Ca(2+) levels, binds calcium which triggers a conformational change (PubMed:23351007). This conformational change allows interaction of S1001A with specific target proteins, such as TPR- containing proteins, and the modulation of their activity (PubMed:22399290). {ECO:0000269|PubMed:22399290, ECO:0000269|PubMed:23351007}.;
Pathway
Toll-Like Receptors Cascades;Innate Immune System;Immune System;Regulation of TLR by endogenous ligand (Consensus)

Recessive Scores

pRec
0.126

Intolerance Scores

loftool
0.666
rvis_EVS
-0.1
rvis_percentile_EVS
46.2

Haploinsufficiency Scores

pHI
0.236
hipred
N
hipred_score
0.439
ghis
0.382

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.731

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
S100a1
Phenotype
normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;toll-like receptor signaling pathway;regulation of heart contraction;substantia nigra development;intracellular signal transduction;positive regulation of nitric-oxide synthase activity;positive regulation of voltage-gated calcium channel activity;positive regulation of sprouting angiogenesis
Cellular component
extracellular region;nucleus;sarcoplasmic reticulum;Z disc;M band;protein-containing complex;neuron projection
Molecular function
calcium ion binding;protein binding;identical protein binding;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding;ATPase binding