S100A16

protein-coding

S100 calcium binding protein A16, the group of S100 calcium binding proteins|EF-hand domain containing

Gene summary

Enables calcium ion binding activity and protein homodimerization activity. Predicted to act upstream of or within response to calcium ion. Located in cytosol; nucleolus; and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_080388.3

Inheritance

—

ClinVar variants

U:13B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr1:153,606,886-153,613,145

External References & Databases

Ensembl (ENSG00000188643)

Transcript & Mutation Effects

hg38 • Region Span ~6.3 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 S100A16 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080388.3. 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			10 clinvar	2 clinvar		12
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	13	2	0	15

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080388.3	RefSeq	NP_525127.1	2	MANE Select
ENST00000368706.9	Ensembl	ENSP00000357695.3	2	MANE Select
NM_001317007.1	RefSeq	NP_001303936.1	2	Standard
NM_001317008.2	RefSeq	NP_001303937.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to calcium ion

Molecular Function

RNA binding
calcium ion binding
protein binding
protein homodimerization activity

Cellular Component

extracellular space
nucleolus
cytosol
plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368704
Coding exons: 2
Length: 6260
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125735
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.512	76	64.4	1.18	0.00000387	691
Missense (PolyPhen)		22	16.937	1.2989		208
Synonymous	0.205	25	26.3	0.949	0.00000164	180
Loss of Function	-0.313	4	3.38	1.18	1.41e-7	46

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-binding protein. Binds one calcium ion per monomer (PubMed:17030513). Can promote differentiation of adipocytes (in vitro) (By similarity). Overexpression in preadipocytes increases their proliferation, enhances adipogenesis and reduces insulin-stimulated glucose uptake (By similarity). {ECO:0000250|UniProtKB:Q9D708, ECO:0000269|PubMed:17030513}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.679
RVIS EVS: -0.14
RVIS percentile EVS: 42.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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