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GeneBe

S100A7

S100 calcium binding protein A7, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153457743-153460651

Previous symbols: [ "PSOR1" ]

Links

ENSG00000143556NCBI:6278OMIM:600353HGNC:10497Uniprot:P31151AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A7 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 S100A7 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
2
clinvar
2
clinvar
4
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 2 0

Variants in S100A7

This is a list of pathogenic ClinVar variants found in the S100A7 region.

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

Position Type Phenotype Significance ClinVar
1-153457903-A-G Inborn genetic diseases Uncertain significance (Nov 08, 2021)2344109
1-153457943-C-T Inborn genetic diseases Likely benign (Jun 23, 2023)2592680
1-153458946-C-T Inborn genetic diseases Uncertain significance (Aug 05, 2023)2596044
1-153458959-T-G Likely benign (May 01, 2023)2639348

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A7protein_codingprotein_codingENST00000368723 22958
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4530.45800000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4896958.51.180.00000316688
Missense in Polyphen1112.6360.87055191
Synonymous-0.4962623.01.130.00000145168
Loss of Function1.1401.520.006.32e-821

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)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Pathway
IL-17 signaling pathway - Homo sapiens (human);Neutrophil degranulation;Antimicrobial peptides;Innate Immune System;Immune System;Validated targets of C-MYC transcriptional repression;Metal sequestration by antimicrobial proteins (Consensus)

Intolerance Scores

loftool
rvis_EVS
0.37
rvis_percentile_EVS
74.95

Haploinsufficiency Scores

pHI
0.0959
hipred
N
hipred_score
0.254
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.589

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Gene ontology

Biological process
response to reactive oxygen species;angiogenesis;epidermis development;positive regulation of T cell chemotaxis;antimicrobial humoral response;keratinocyte differentiation;response to lipopolysaccharide;neutrophil degranulation;innate immune response;defense response to Gram-negative bacterium;sequestering of metal ion;antimicrobial humoral immune response mediated by antimicrobial peptide;positive regulation of ERK1 and ERK2 cascade;positive regulation of granulocyte chemotaxis;positive regulation of monocyte chemotaxis
Cellular component
extracellular region;extracellular space;nucleus;cytoplasm;endoplasmic reticulum;cytosol;focal adhesion;azurophil granule lumen;collagen-containing extracellular matrix
Molecular function
calcium ion binding;protein binding;zinc ion binding;RAGE receptor binding