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GeneBe

S100A4

S100 calcium binding protein A4, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:153543612-153550136

Previous symbols: [ "MTS1", "CAPL" ]

Links

ENSG00000196154NCBI:6275OMIM:114210HGNC:10494Uniprot:P26447AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A4 gene.

  • not provided (4 variants)
  • Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A4 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
4
clinvar
4
missense
2
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 2 0 4

Variants in S100A4

This is a list of pathogenic ClinVar variants found in the S100A4 region.

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

Position Type Phenotype Significance ClinVar
1-153543831-G-A Benign (Dec 31, 2019)777935
1-153543860-C-T Inborn genetic diseases Uncertain significance (Oct 12, 2021)2361875
1-153543861-G-A Benign (Mar 02, 2018)736033
1-153543882-G-A Benign (Dec 31, 2019)772816
1-153544656-C-T Inborn genetic diseases Uncertain significance (Jan 03, 2022)2268926
1-153544735-C-T Benign (Dec 31, 2019)786858
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
S100A4protein_codingprotein_codingENST00000368716 26524
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.006180.5191257060411257470.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3654855.70.8620.00000288682
Missense in Polyphen1315.5320.837215
Synonymous0.6991923.30.8160.00000137171
Loss of Function-0.035732.931.021.22e-743

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001520.000152
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001390.000139
European (Non-Finnish)0.0002550.000255
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.0006520.000652

dbNSFP

Source: dbNSFP

Pathway
Vitamin D Receptor Pathway (Consensus)

Recessive Scores

pRec
0.520

Intolerance Scores

loftool
0.817
rvis_EVS
-0.19
rvis_percentile_EVS
39.68

Haploinsufficiency Scores

pHI
0.262
hipred
Y
hipred_score
0.778
ghis
0.610

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.815

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
S100a4
Phenotype
immune system phenotype; cellular phenotype; neoplasm; hematopoietic system 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); normal phenotype;

Gene ontology

Biological process
epithelial to mesenchymal transition;positive regulation of I-kappaB kinase/NF-kappaB signaling
Cellular component
extracellular region;extracellular space;nucleus;neuron projection;perinuclear region of cytoplasm;extracellular exosome
Molecular function
RNA binding;actin binding;calcium ion binding;protein binding;identical protein binding;transition metal ion binding;calcium-dependent protein binding;RAGE receptor binding