S100A11

S100 calcium binding protein A11, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:152032505-152047907

Links

ENSG00000163191 ∙ NCBI:6282 ∙ OMIM:603114 ∙ HGNC:10488 ∙ Uniprot:P31949 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A11 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A11 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	3	0	0

Variants in S100A11

This is a list of pathogenic ClinVar variants found in the S100A11 region.

Position	Type	Phenotype	Significance	ClinVar
1-152032688-C-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2021)
1-152032745-C-T		Inborn genetic diseases	Uncertain significance (Apr 22, 2022)
1-152032768-C-G		Inborn genetic diseases	Uncertain significance (May 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A11	protein_coding	protein_coding	ENST00000271638	3	15402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00847	0.586	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.309	51	57.6	0.885	0.00000292	693
Missense in Polyphen		7	11.605	0.60317		190
Synonymous	0.580	18	21.4	0.841	9.87e-7	203
Loss of Function	0.225	3	3.45	0.869	1.45e-7	45

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00223
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitates the differentiation and the cornification of keratinocytes. {ECO:0000269|PubMed:18618420}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• loftool: 0.575
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.506
• ghis: 0.501

Essentials

• essential_gene_CRISPR: 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: S100a11
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: signal transduction;negative regulation of DNA replication;negative regulation of cell population proliferation;neutrophil degranulation;cell-cell adhesion
• Cellular component: ruffle;extracellular region;extracellular space;nucleus;cytoplasm;cell-cell adherens junction;secretory granule lumen;extracellular exosome
• Molecular function: calcium ion binding;protein binding;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding;cadherin binding involved in cell-cell adhesion