S100A10

S100 calcium binding protein A10, the group of S100 calcium binding proteins

Basic information

Region (hg38): 1:151982914-151993859

Previous symbols: [ "ANX2LG", "CAL1L" ]

Links

ENSG00000197747 ∙ NCBI:6281 ∙ OMIM:114085 ∙ HGNC:10487 ∙ Uniprot:P60903 ∙ 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 S100A10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A10 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in S100A10

This is a list of pathogenic ClinVar variants found in the S100A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151986178-T-G		not specified	Uncertain significance (Mar 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A10	protein_coding	protein_coding	ENST00000368811	2	11476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.168	0.654	116709	0	1	116710	0.00000428

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	35	48.4	0.724	0.00000221	657
Missense in Polyphen		0	4.125	0		78
Synonymous	-0.126	18	17.3	1.04	9.87e-7	157
Loss of Function	0.808	1	2.33	0.429	9.59e-8	39

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000651	0.0000651
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Because S100A10 induces the dimerization of ANXA2/p36, it may function as a regulator of protein phosphorylation in that the ANXA2 monomer is the preferred target (in vitro) of tyrosine- specific kinase.
• Pathway: Prostaglandin Synthesis and Regulation;Dissolution of Fibrin Clot;EGFR1;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.292

Intolerance Scores

• loftool: 0.385
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.552
• hipred: Y
• hipred_score: 0.506
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a10
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: membrane raft assembly;vesicle budding from membrane;positive regulation of GTPase activity;positive regulation of binding;protein heterotetramerization;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;protein localization to plasma membrane;positive regulation of substrate adhesion-dependent cell spreading
• Cellular component: extracellular region;extrinsic component of plasma membrane;membrane raft;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: calcium ion binding;protein binding;lipid binding;protein homodimerization activity;ion channel binding