S100A13

S100 calcium binding protein A13, the group of S100 calcium binding proteins

Basic information

Region (hg38): 1:153618786-153631360

Links

ENSG00000189171 ∙ NCBI:6284 ∙ OMIM:601989 ∙ HGNC:10490 ∙ Uniprot:Q99584 ∙ 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 S100A13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A13 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			7	1		8
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in S100A13

This is a list of pathogenic ClinVar variants found in the S100A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153618908-A-G		not specified	Uncertain significance (Jan 04, 2024)
1-153618950-CCAAT-C			Uncertain significance (Mar 26, 2024)
1-153618971-T-C		not specified	Uncertain significance (May 06, 2022)
1-153618986-G-A		not specified	Uncertain significance (Sep 28, 2022)
1-153618994-A-T		not specified	Uncertain significance (Dec 01, 2022)
1-153626370-C-T		not specified	Likely benign (Aug 02, 2022)
1-153626390-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-153626420-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-153626453-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-153630581-G-A			Benign (Jun 12, 2018)
1-153630640-C-T		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A13	protein_coding	protein_coding	ENST00000368699	2	15306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0497	0.703	125727	0	16	125743	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.315	46	52.4	0.877	0.00000270	649
Missense in Polyphen		9	15.9	0.56602		206
Synonymous	0.465	20	22.8	0.876	0.00000134	180
Loss of Function	0.656	2	3.28	0.609	1.38e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000457	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the export of proteins that lack a signal peptide and are secreted by an alternative pathway. Binds two calcium ions per subunit. Binds one copper ion. Binding of one copper ion does not interfere with calcium binding. Required for the copper-dependent stress-induced export of IL1A and FGF1. The calcium-free protein binds to lipid vesicles containing phosphatidylserine, but not to vesicles containing phosphatidylcholine (By similarity). {ECO:0000250, ECO:0000269|PubMed:12746488, ECO:0000269|PubMed:20863990}.

Intolerance Scores

• loftool: 0.817
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.245
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a13

Gene ontology

• Biological process: positive regulation of cell population proliferation;regulation of cell shape;positive regulation of I-kappaB kinase/NF-kappaB signaling;mast cell degranulation;response to copper ion;cytokine secretion;interleukin-1 alpha secretion;response to electrical stimulus
• Cellular component: extracellular region;extracellular space;nucleus;nucleolus;cytoplasm;cytosol;plasma membrane;mast cell granule;perinuclear region of cytoplasm
• Molecular function: copper ion binding;calcium ion binding;protein binding;zinc ion binding;lipid binding;fibroblast growth factor binding;protein homodimerization activity;RAGE receptor binding