S100A2

S100 calcium binding protein A2, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:153561107-153567890

Previous symbols: [ "S100L" ]

Links

ENSG00000196754 ∙ NCBI:6273 ∙ OMIM:176993 ∙ HGNC:10492 ∙ Uniprot:P29034 ∙ 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 S100A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A2 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			1		1	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	1

Variants in S100A2

This is a list of pathogenic ClinVar variants found in the S100A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153563852-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-153563870-C-G			Benign (Jul 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A2	protein_coding	protein_coding	ENST00000368708	2	6783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000584	0.156	125672	0	63	125735	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0387	49	49.8	0.985	0.00000231	645
Missense in Polyphen		18	14.123	1.2745		196
Synonymous	-0.428	24	21.5	1.12	0.00000111	175
Loss of Function	-1.47	5	2.50	2.00	1.05e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000809	0.000809
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000294	0.000294
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as calcium sensor and modulator, contributing to cellular calcium signaling. May function by interacting with other proteins, such as TPR-containing proteins, and indirectly play a role in many physiological processes. May also play a role in suppressing tumor cell growth. {ECO:0000269|PubMed:1372446, ECO:0000269|PubMed:22399290}.
• Pathway: Vitamin D Receptor Pathway;p73 transcription factor network;Validated transcriptional targets of TAp63 isoforms;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.674
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.461
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.601

Gene Damage Prediction

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

Gene ontology

• Biological process: endothelial cell migration
• Cellular component: cellular_component
• Molecular function: calcium ion binding;protein binding;identical protein binding;transition metal ion binding