RGN
regucalcin
Basic information
Region (hg38): X:47078355-47093314
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (42 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152869.4. 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 | |||||
| missense | 41 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RGN | protein_coding | protein_coding | ENST00000397180 | 6 | 14938 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0221 | 0.916 | 125711 | 12 | 21 | 125744 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.913 | 138 | 111 | 1.24 | 0.00000868 | 1939 |
| Missense in Polyphen | 43 | 37.541 | 1.1454 | 642 | ||
| Synonymous | 0.190 | 41 | 42.6 | 0.963 | 0.00000344 | 578 |
| Loss of Function | 1.60 | 4 | 9.23 | 0.433 | 6.54e-7 | 177 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000337 | 0.000306 |
| Ashkenazi Jewish | 0.000808 | 0.000595 |
| East Asian | 0.000146 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000164 | 0.000114 |
| Middle Eastern | 0.000146 | 0.000109 |
| South Asian | 0.000267 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Gluconolactonase with low activity towards other sugar lactones, including gulonolactone and galactonolactone. Can also hydrolyze diisopropyl phosphorofluoridate and phenylacetate (in vitro). Calcium-binding protein. Modulates Ca(2+) signaling, and Ca(2+)-dependent cellular processes and enzyme activities (By similarity). {ECO:0000250}.;
- Pathway
- Ascorbate and aldarate metabolism - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.344
Intolerance Scores
- loftool
- 0.396
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.22
Haploinsufficiency Scores
- pHI
- 0.127
- hipred
- N
- hipred_score
- 0.398
- ghis
- 0.447
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.908
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rgn
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); 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); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; cellular phenotype; skeleton phenotype; growth/size/body region 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- kidney development;negative regulation of protein kinase activity;cellular calcium ion homeostasis;spermatogenesis;aging;positive regulation of triglyceride biosynthetic process;positive regulation of glucose metabolic process;positive regulation of phosphatase activity;L-ascorbic acid biosynthetic process;negative regulation of phosphoprotein phosphatase activity;positive regulation of ATPase activity;negative regulation of GTPase activity;negative regulation of apoptotic process;positive regulation of GTPase activity;negative regulation of nitric oxide biosynthetic process;positive regulation of fatty acid biosynthetic process;negative regulation of epithelial cell proliferation;regulation of calcium-mediated signaling;negative regulation of cyclic-nucleotide phosphodiesterase activity;liver regeneration;negative regulation of flagellated sperm motility;positive regulation of superoxide dismutase activity;positive regulation of calcium-transporting ATPase activity;negative regulation of RNA biosynthetic process;negative regulation of bone development;positive regulation of proteolysis involved in cellular protein catabolic process;negative regulation of calcium-dependent ATPase activity;negative regulation of DNA catabolic process;positive regulation of dUTP diphosphatase activity;negative regulation of leucine-tRNA ligase activity;negative regulation of DNA biosynthetic process
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- gluconolactonase activity;calcium ion binding;zinc ion binding;enzyme regulator activity