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 ∙ ClinVar

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)

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.

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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in S100A3

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

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

Position	Type	Phenotype	Significance	ClinVar
1-153547699-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-153547710-C-A		not specified	Uncertain significance (Dec 19, 2023)
1-153547718-G-C		not specified	Uncertain significance (Jun 29, 2022)
1-153547759-G-A			Benign (Apr 04, 2024)
1-153547804-G-C			Likely benign (Mar 01, 2024)
1-153547821-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-153547833-T-C		not specified	Uncertain significance (Mar 08, 2024)
1-153547845-G-C		not specified	Uncertain significance (Jan 10, 2022)
1-153548428-C-T		not specified	Uncertain significance (Nov 09, 2023)
1-153548449-C-A		not specified	Uncertain significance (Jun 29, 2022)
1-153548461-C-A		Malignant tumor of prostate	Uncertain significance (-)
1-153548463-G-A		not specified	Uncertain significance (Jan 04, 2022)

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