S100A3
protein-codingS100 calcium binding protein A3, the group of S100 calcium binding proteins
Gene summary
The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein has the highest content of cysteines of all S100 proteins, has a high affinity for Zinc, and is highly expressed in human hair cuticle. The precise function of this protein is unknown. [provided by RefSeq, Jul 2008]
- S100E
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to S100A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002960.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 15 | 1 | 1 | 17 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 15 | 1 | 1 | 17 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002951.1 | 2 | MANE Select | |
| Ensembl | ENSP00000357702.3 | 2 | MANE Select | |
| Ensembl | ENSP00000357701.1 | 2 | Standard | |
| Ensembl | ENSP00000357701.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- calcium ion binding
- zinc ion binding
Cellular Component
- nucleolus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368713
- Coding exons
- 2
- Length
- 2044
- Individuals with no LoFs
- 125003
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 725
- Defined
- 125731
- p
- 0.00290
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0726 | 61 | 59.4 | 1.03 | 0.00000348 | 650 |
| Missense (PolyPhen) | 13 | 13.905 | 0.93492 | 173 | ||
| Synonymous | 0.468 | 22 | 25.0 | 0.881 | 0.00000150 | 183 |
| Loss of Function | 0.172 | 3 | 3.34 | 0.898 | 1.41e-7 | 41 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00092 | 0.00092 | rare |
| Latino/Admixed American | 0.0018 | 0.0017 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00055 | 0.00055 | rare |
| European (Non-Finnish) | 0.0055 | 0.0055 | notable |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.0024 | 0.0024 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds both calcium and zinc. May be involved in calcium- dependent cuticle cell differentiation, hair shaft and hair cuticular barrier formation. {ECO:0000269|PubMed:18083705}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.715
- RVIS EVS
- 0.61
- RVIS percentile EVS
- 83.07
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.911
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |