S100A3

S100 calcium binding protein A3, the group of S100 calcium binding proteins

Basic information

Region (hg38): 1:153547328-153549258

Previous symbols: [ "S100E" ]

Links

ENSG00000188015 ∙ NCBI:6274 ∙ OMIM:176992 ∙ HGNC:10493 ∙ Uniprot:P33764 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A3 gene.

• Inborn genetic diseases (3 variants)
• Malignant tumor of prostate (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A3 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	4	0	0

Variants in S100A3

This is a list of pathogenic ClinVar variants found in the S100A3 region.

Position	Type	Phenotype	Significance	ClinVar
1-153547718-G-C		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
1-153547845-G-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2022)
1-153548449-C-A		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
1-153548461-C-A		Malignant tumor of prostate	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A3	protein_coding	protein_coding	ENST00000368713	2	2044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00793	0.572	125003	3	725	125731	0.00290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0726	61	59.4	1.03	0.00000348	650
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00269	0.00269
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000554	0.000554
European (Non-Finnish)	0.00551	0.00552
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00245	0.00245

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.0946
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: S100a3

Gene ontology

• Cellular component: nucleolus;cytosol
• Molecular function: calcium ion binding;zinc ion binding