S100A13

protein-coding

S100 calcium binding protein A13, 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 is widely expressed in various types of tissues with a high expression level in thyroid gland. In smooth muscle cells, this protein co-expresses with other family members in the nucleus and in stress fibers, suggesting diverse functions in signal transduction. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001024211.2

Inheritance

—

ClinVar variants

U:16B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr1:153,618,779-153,634,412

External References & Databases

Ensembl (ENSG00000189171)

Transcript & Mutation Effects

hg38 • Region Span ~15.6 kb

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GenCC 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 S100A13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 15

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001024211.2. 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			14 clinvar	2 clinvar		16
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	16	2	0	18

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 118 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001024211.2	RefSeq	NP_001019382.1	2	MANE Select
ENST00000476133.6	Ensembl	ENSP00000507299.1	2	MANE Select
NM_001024210.2	RefSeq	NP_001019381.1	2	Standard
NM_001024212.2	RefSeq	NP_001019383.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

copper ion binding
calcium ion binding
protein binding
zinc ion binding
lipid binding

Cellular Component

extracellular region
extracellular space
nucleus
nucleolus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368699
Coding exons: 2
Length: 15306
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125743
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.315	46	52.4	0.877	0.00000270	649
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.00046	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.978

Gene Damage Prediction

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