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GeneBe

S100A5

S100 calcium binding protein A5, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153537146-153541765

Previous symbols: [ "S100D" ]

Links

ENSG00000196420NCBI:6276OMIM:176991HGNC:10495Uniprot:P33763AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A5 gene.

  • Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A5 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
6
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 0 0

Variants in S100A5

This is a list of pathogenic ClinVar variants found in the S100A5 region.

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

Position Type Phenotype Significance ClinVar
1-153537324-T-C not specified Uncertain significance (Sep 30, 2021)2372984
1-153537384-T-A not specified Uncertain significance (Mar 16, 2022)2278475
1-153537385-C-T not specified Uncertain significance (Mar 23, 2022)2406436
1-153537419-G-C not specified Uncertain significance (Jan 05, 2022)2349805
1-153537425-G-C not specified Uncertain significance (Oct 02, 2023)3157401
1-153540101-T-A not specified Uncertain significance (Jan 09, 2024)3157404
1-153540119-T-C not specified Uncertain significance (May 13, 2022)2289639
1-153540133-G-A not specified Uncertain significance (Jan 30, 2024)3157402
1-153540157-A-G not specified Uncertain significance (Sep 28, 2022)2223741

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100A5protein_codingprotein_codingENST00000368718 24619
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00005510.151125738091257470.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1325451.31.050.00000266620
Missense in Polyphen1617.6410.90698211
Synonymous-0.6462723.11.170.00000152157
Loss of Function-1.5352.432.069.96e-840

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001480.000148
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds calcium, zinc and copper. One subunit can simultaneously bind 2 calcium ions or 2 copper ions plus 1 zinc ion. Calcium and copper ions compete for the same binding sites. {ECO:0000269|PubMed:10882717}.;

Recessive Scores

pRec
0.117

Intolerance Scores

loftool
0.662
rvis_EVS
0.39
rvis_percentile_EVS
75.87

Haploinsufficiency Scores

pHI
0.0650
hipred
N
hipred_score
0.170
ghis
0.398

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.150

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
S100a5
Phenotype
taste/olfaction phenotype; normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process
Cellular component
nucleus;neuronal cell body
Molecular function
copper ion binding;calcium ion binding;zinc ion binding;protein homodimerization activity