S100A1

S100 calcium binding protein A1, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153627925-153632039

Previous symbols: [ "S100A" ]

Links

ENSG00000160678 ∙ NCBI:6271 ∙ OMIM:176940 ∙ HGNC:10486 ∙ Uniprot:P23297 ∙ 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 S100A1 gene.

• Inborn genetic diseases (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A1 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	2	0	1

Variants in S100A1

This is a list of pathogenic ClinVar variants found in the S100A1 region.

Position	Type	Phenotype	Significance	ClinVar
1-153630581-G-A			Benign (Jun 12, 2018)
1-153630640-C-T		Inborn genetic diseases	Uncertain significance (Jun 12, 2023)
1-153631727-G-T		Inborn genetic diseases	Uncertain significance (Nov 22, 2022)
1-153631798-C-T		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A1	protein_coding	protein_coding	ENST00000292169	2	4112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00600	0.513	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.155	57	53.8	1.06	0.00000296	624
Missense in Polyphen		24	18.699	1.2835		231
Synonymous	-0.133	27	26.1	1.03	0.00000185	174
Loss of Function	-0.0615	3	2.89	1.04	1.20e-7	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably acts as a Ca(2+) signal transducer (PubMed:22399290). In response to an increase in intracellular Ca(2+) levels, binds calcium which triggers a conformational change (PubMed:23351007). This conformational change allows interaction of S1001A with specific target proteins, such as TPR- containing proteins, and the modulation of their activity (PubMed:22399290). {ECO:0000269|PubMed:22399290, ECO:0000269|PubMed:23351007}.
• Pathway: Toll-Like Receptors Cascades;Innate Immune System;Immune System;Regulation of TLR by endogenous ligand (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.666
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.439
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a1
• Phenotype: normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); respiratory system phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;toll-like receptor signaling pathway;regulation of heart contraction;substantia nigra development;intracellular signal transduction;positive regulation of nitric-oxide synthase activity;positive regulation of voltage-gated calcium channel activity;positive regulation of sprouting angiogenesis
• Cellular component: extracellular region;nucleus;sarcoplasmic reticulum;Z disc;M band;protein-containing complex;neuron projection
• Molecular function: calcium ion binding;protein binding;identical protein binding;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding;ATPase binding