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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100A2 gene.

• not provided (1 variants)

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.

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

Variants in S100A2

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

Position	Type	Phenotype	Significance	ClinVar
1-153563852-G-A		Inborn genetic diseases	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