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 ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in S100A11

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

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

Position	Type	Phenotype	Significance	ClinVar
1-152032688-C-G		not specified	Uncertain significance (Jul 26, 2021)
1-152032745-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-152032768-C-G		not specified	Uncertain significance (May 05, 2022)
1-152033713-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-152033781-G-A		not specified	Uncertain significance (Dec 12, 2023)

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