S100A7

S100 calcium binding protein A7, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153457743-153460651

Previous symbols: [ "PSOR1" ]

Links

ENSG00000143556 ∙ NCBI:6278 ∙ OMIM:600353 ∙ HGNC:10497 ∙ Uniprot:P31151 ∙ 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 S100A7 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A7 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			2	2		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	2	2	0

Variants in S100A7

This is a list of pathogenic ClinVar variants found in the S100A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153457903-A-G		not specified	Uncertain significance (Nov 08, 2021)
1-153457943-C-T		not specified	Likely benign (Jun 23, 2023)
1-153458946-C-T		not specified	Uncertain significance (Aug 05, 2023)
1-153458959-T-G			Likely benign (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A7	protein_coding	protein_coding	ENST00000368723	2	2958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.453	0.458	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.489	69	58.5	1.18	0.00000316	688
Missense in Polyphen		11	12.636	0.87055		191
Synonymous	-0.496	26	23.0	1.13	0.00000145	168
Loss of Function	1.14	0	1.52	0.00	6.32e-8	21

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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

• Pathway: IL-17 signaling pathway - Homo sapiens (human);Neutrophil degranulation;Antimicrobial peptides;Innate Immune System;Immune System;Validated targets of C-MYC transcriptional repression;Metal sequestration by antimicrobial proteins (Consensus)

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.0959
• hipred: N
• hipred_score: 0.254

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

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

Gene ontology

• Biological process: response to reactive oxygen species;angiogenesis;epidermis development;positive regulation of T cell chemotaxis;antimicrobial humoral response;keratinocyte differentiation;response to lipopolysaccharide;neutrophil degranulation;innate immune response;defense response to Gram-negative bacterium;sequestering of metal ion;antimicrobial humoral immune response mediated by antimicrobial peptide;positive regulation of ERK1 and ERK2 cascade;positive regulation of granulocyte chemotaxis;positive regulation of monocyte chemotaxis
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;endoplasmic reticulum;cytosol;focal adhesion;azurophil granule lumen;collagen-containing extracellular matrix
• Molecular function: calcium ion binding;protein binding;zinc ion binding;RAGE receptor binding