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 ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A1 gene.

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.

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					1	1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	1

Variants in S100A1

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

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

Position	Type	Phenotype	Significance	ClinVar
1-153630581-G-A			Benign (Jun 12, 2018)
1-153630640-C-T		not specified	Uncertain significance (Jun 12, 2023)
1-153631727-G-T		not specified	Uncertain significance (Nov 22, 2022)
1-153631798-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-153631835-C-G		not specified	Uncertain significance (Dec 27, 2023)

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