S100A6

S100 calcium binding protein A6, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:153534598-153536244

Previous symbols: [ "CACY" ]

Links

ENSG00000197956 ∙ NCBI:6277 ∙ OMIM:114110 ∙ HGNC:10496 ∙ Uniprot:P06703 ∙ 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 S100A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A6 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			6		1	7
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	7	0	1

Variants in S100A6

This is a list of pathogenic ClinVar variants found in the S100A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153534700-C-T			Benign (Apr 24, 2018)
1-153534779-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-153534787-TC-T		not specified	Uncertain significance (Jan 06, 2020)
1-153534817-G-A		not specified	Uncertain significance (Jul 26, 2023)
1-153535203-G-A		not specified	Uncertain significance (Aug 15, 2023)
1-153535279-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-153535303-C-T		not specified	Uncertain significance (Apr 21, 2022)
1-153535336-C-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A6	protein_coding	protein_coding	ENST00000368720	2	1646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.176	0.656	125734	0	4	125738	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.246	43	47.8	0.900	0.00000244	587
Missense in Polyphen		9	9.6226	0.9353		136
Synonymous	0.915	16	21.4	0.748	0.00000108	173
Loss of Function	0.853	1	2.44	0.410	1.02e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as calcium sensor and modulator, contributing to cellular calcium signaling. May function by interacting with other proteins, such as TPR-containing proteins, and indirectly play a role in many physiological processes such as the reorganization of the actin cytoskeleton and in cell motility. Binds 2 calcium ions. Calcium binding is cooperative. {ECO:0000269|PubMed:22399290}.
• Pathway: Gastric Cancer Network 2;Vitamin D Receptor Pathway;Prostaglandin Synthesis and Regulation (Consensus)

Recessive Scores

• pRec: 0.586

Intolerance Scores

• loftool: 0.562
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.67

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.702
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a6
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: signal transduction;axonogenesis;ion transmembrane transport;positive regulation of fibroblast proliferation
• Cellular component: ruffle;extracellular region;nucleus;nuclear envelope;cytoplasm;cytosol;plasma membrane;extrinsic component of cytoplasmic side of plasma membrane;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: calcium ion binding;protein binding;tropomyosin binding;zinc ion binding;ion transmembrane transporter activity;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding