STC1

stanniocalcin 1

Basic information

Region (hg38): 8:23841929-23854806

Previous symbols: [ "STC" ]

Links

ENSG00000159167

∙ NCBI:6781 ∙ OMIM:601185 ∙ HGNC:11373 ∙ Uniprot:P52823 ∙ 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 STC1 gene.

not_specified (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003155.3. 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						0
missense			18 clinvar	1 clinvar		19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STC1	protein_coding	protein_coding	ENST00000290271	4	12893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.204	0.788	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	87	143	0.608	0.00000814	1635
Missense in Polyphen		35	53.89	0.64948		607
Synonymous	0.264	55	57.5	0.956	0.00000330	485
Loss of Function	2.26	3	11.2	0.269	7.50e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Stimulates renal phosphate reabsorption, and could therefore prevent hypercalcemia.;
Pathway: Ectoderm Differentiation (Consensus)

Intolerance Scores

loftool: 0.181
rvis_EVS: -0.14
rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

pHI: 0.861
hipred: Y
hipred_score: 0.800
ghis: 0.493

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Stc1
Phenotype: reproductive system phenotype; normal phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;

Zebrafish Information Network

Gene name: stc1l
Affected structure: NCC ionocyte
Phenotype tag: abnormal
Phenotype quality: increased amount

Gene ontology

Biological process: ossification;endothelial cell morphogenesis;growth plate cartilage axis specification;cellular calcium ion homeostasis;embryo implantation;regulation of signaling receptor activity;negative regulation of endothelial cell migration;negative regulation of cell migration;response to vitamin D;chondrocyte proliferation;regulation of anion transport;decidualization;negative regulation of calcium ion transport;bone development;cellular response to cAMP;cellular response to glucocorticoid stimulus;cellular response to hypoxia;regulation of cardiac muscle cell contraction;positive regulation of calcium ion import;negative regulation of renal phosphate excretion
Cellular component: extracellular space;nucleus;cytoplasm;apical plasma membrane
Molecular function: hormone activity