STC2

stanniocalcin 2

Basic information

Region (hg38): 5:173314723-173328447

Links

ENSG00000113739

∙ NCBI:8614 ∙ OMIM:603665 ∙ HGNC:11374 ∙ Uniprot:O76061 ∙ 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 STC2 gene.

not_specified (30 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003714.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STC2	protein_coding	protein_coding	ENST00000265087	4	14791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.266	0.729	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	141	187	0.753	0.0000115	1980
Missense in Polyphen		36	70.79	0.50855		846
Synonymous	0.282	77	80.2	0.960	0.00000541	593
Loss of Function	2.42	3	12.1	0.248	7.69e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000143	0.000139
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Has an anti-hypocalcemic action on calcium and phosphate homeostasis.;
Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

pRec: 0.162

Intolerance Scores

loftool: 0.0329
rvis_EVS: -0.54
rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

pHI: 0.145
hipred: Y
hipred_score: 0.800
ghis: 0.469

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Stc2
Phenotype: reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: cellular calcium ion homeostasis;response to oxidative stress;embryo implantation;regulation of signaling receptor activity;negative regulation of gene expression;endoplasmic reticulum unfolded protein response;response to vitamin D;negative regulation of multicellular organism growth;response to peptide hormone;post-translational protein modification;cellular protein metabolic process;decidualization;regulation of hormone biosynthetic process;cellular response to hypoxia;regulation of store-operated calcium entry
Cellular component: extracellular space;endoplasmic reticulum;endoplasmic reticulum lumen;Golgi apparatus;perinuclear region of cytoplasm
Molecular function: hormone activity;enzyme binding;heme binding;protein homodimerization activity