STIM2

stromal interaction molecule 2, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 4:26857601-27025381

Links

ENSG00000109689 ∙ NCBI:57620 ∙ OMIM:610841 ∙ HGNC:19205 ∙ Uniprot:Q9P246 ∙ 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 STIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STIM2 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			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	0	0

Variants in STIM2

This is a list of pathogenic ClinVar variants found in the STIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-26861241-T-C		not specified	Uncertain significance (Dec 09, 2024)
4-26861261-T-C		not specified	Uncertain significance (Aug 23, 2021)
4-26861274-C-G		not specified	Uncertain significance (Mar 27, 2023)
4-26861274-C-T		not specified	Uncertain significance (Sep 29, 2023)
4-26861279-C-A		not specified	Uncertain significance (Dec 03, 2021)
4-26861282-C-T		not specified	Uncertain significance (Nov 21, 2022)
4-26861286-G-A		not specified	Uncertain significance (Dec 19, 2022)
4-26861313-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-26861325-C-T		not specified	Uncertain significance (Apr 29, 2024)
4-26861333-G-A		not specified	Uncertain significance (Dec 03, 2024)
4-26861360-C-T		not specified	Uncertain significance (May 15, 2024)
4-26861363-A-G		not specified	Uncertain significance (Nov 09, 2022)
4-26861364-T-A		not specified	Uncertain significance (May 31, 2023)
4-26861367-C-G		not specified	Uncertain significance (Oct 08, 2024)
4-26919563-G-A		not specified	Uncertain significance (Dec 21, 2021)
4-26919585-A-G		not specified	Uncertain significance (Aug 08, 2023)
4-26957675-G-A		not specified	Uncertain significance (Aug 02, 2021)
4-26957675-G-T		not specified	Uncertain significance (Jul 25, 2024)
4-26957682-A-G		not specified	Uncertain significance (Jun 13, 2024)
4-26957684-A-G		not specified	Uncertain significance (Jul 30, 2024)
4-26995435-C-G		not specified	Uncertain significance (May 18, 2023)
4-26995466-A-G		not specified	Uncertain significance (Jul 11, 2023)
4-26995478-C-T		not specified	Uncertain significance (Sep 19, 2022)
4-26999264-C-A		not specified	Uncertain significance (Oct 12, 2021)
4-27002219-C-A		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STIM2	protein_coding	protein_coding	ENST00000465503	13	167704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00940	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	324	394	0.823	0.0000210	4935
Missense in Polyphen		118	181.16	0.65134		2352
Synonymous	-0.602	151	142	1.06	0.00000789	1426
Loss of Function	5.02	6	40.5	0.148	0.00000243	461

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000945	0.0000945
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000189	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in mediating store-operated Ca(2+) entry (SOCE), a Ca(2+) influx following depletion of intracellular Ca(2+) stores. Functions as a highly sensitive Ca(2+) sensor in the endoplasmic reticulum which activates both store-operated and store-independent Ca(2+)-influx. Regulates basal cytosolic and endoplasmic reticulum Ca(2+) concentrations. Upon mild variations of the endoplasmic reticulum Ca(2+) concentration, translocates from the endoplasmic reticulum to the plasma membrane where it probably activates the Ca(2+) release-activated Ca(2+) (CRAC) channels ORAI1, ORAI2 and ORAI3. May inhibit STIM1-mediated Ca(2+) influx. {ECO:0000269|PubMed:16005298, ECO:0000269|PubMed:16860747, ECO:0000269|PubMed:17905723, ECO:0000269|PubMed:18160041, ECO:0000269|PubMed:21217057, ECO:0000269|PubMed:22464749, ECO:0000269|PubMed:23359669}.
• Pathway: Calcium signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.41

Haploinsufficiency Scores

• pHI: 0.151
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stim2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: store-operated calcium entry;cellular calcium ion homeostasis;activation of store-operated calcium channel activity;positive regulation of calcium ion transport;calcium ion transmembrane transport
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: calcium channel regulator activity;calcium ion binding;protein binding;store-operated calcium channel activity