S100A16

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

Basic information

Region (hg38): 1:153606886-153613145

Links

ENSG00000188643 ∙ NCBI:140576 ∙ OMIM:617437 ∙ HGNC:20441 ∙ Uniprot:Q96FQ6 ∙ 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 S100A16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A16 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in S100A16

This is a list of pathogenic ClinVar variants found in the S100A16 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153607559-T-C		not specified	Uncertain significance (Oct 06, 2021)
1-153607562-T-C		not specified	Likely benign (Sep 27, 2021)
1-153607565-A-T		not specified	Uncertain significance (Nov 22, 2023)
1-153607628-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-153607651-G-T		not specified	Uncertain significance (Dec 06, 2022)
1-153607663-C-G		not specified	Uncertain significance (Feb 17, 2022)
1-153607679-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-153607680-G-A		not specified	Uncertain significance (Oct 06, 2023)
1-153608029-C-T		not specified	Uncertain significance (Nov 15, 2024)
1-153608036-C-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A16	protein_coding	protein_coding	ENST00000368704	2	6260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00106	0.391	125694	0	41	125735	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.512	76	64.4	1.18	0.00000387	691
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000438	0.000438
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.170
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a16

Gene ontology

• Biological process: response to calcium ion
• Cellular component: extracellular space;nucleolus;cytosol;plasma membrane;extracellular exosome
• Molecular function: RNA binding;calcium ion binding;protein binding;protein homodimerization activity