SGK3
serum/glucocorticoid regulated kinase family member 3
Basic information
Region (hg38): 8:66712733-66862022
Previous symbols: [ "SGK2", "SGKL" ]
Links
Phenotypes
GenCC
Source:
- hypophosphatemic rickets (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGK3 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 | 0 | |||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in SGK3
This is a list of pathogenic ClinVar variants found in the SGK3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-66798600-C-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 8-66804396-A-G | not specified | Uncertain significance (Jan 08, 2024) | ||
| 8-66813885-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 8-66822373-C-A | not specified | Uncertain significance (Dec 15, 2023) | ||
| 8-66831277-T-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 8-66835779-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 8-66835781-A-G | not specified | Uncertain significance (Apr 15, 2024) | ||
| 8-66835944-A-G | not specified | Uncertain significance (Dec 15, 2021) | ||
| 8-66840043-A-G | Malignant tumor of prostate | Uncertain significance (-) | ||
| 8-66840051-A-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 8-66840060-G-A | not specified | Uncertain significance (Dec 03, 2021) | ||
| 8-66840093-C-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 8-66843356-T-A | Uncertain significance (Feb 17, 2023) | |||
| 8-66843511-C-G | not specified | Uncertain significance (Mar 01, 2023) | ||
| 8-66847214-G-C | not specified | Uncertain significance (Dec 08, 2023) | ||
| 8-66847233-A-G | not specified | Uncertain significance (Jun 26, 2023) | ||
| 8-66850901-C-A | not specified | Uncertain significance (Jun 07, 2023) | ||
| 8-66859430-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 8-66859498-A-G | not specified | Uncertain significance (Mar 13, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SGK3 | protein_coding | protein_coding | ENST00000396596 | 16 | 149605 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.56e-7 | 0.996 | 125703 | 0 | 40 | 125743 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 180 | 254 | 0.709 | 0.0000120 | 3276 |
| Missense in Polyphen | 60 | 95.765 | 0.62653 | 1236 | ||
| Synonymous | 1.14 | 72 | 85.4 | 0.843 | 0.00000412 | 882 |
| Loss of Function | 2.58 | 15 | 30.3 | 0.494 | 0.00000152 | 379 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000121 | 0.000120 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000258 | 0.000255 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000145 | 0.000131 |
| Other | 0.000165 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine-protein kinase which is involved in the regulation of a wide variety of ion channels, membrane transporters, cell growth, proliferation, survival and migration. Up-regulates Na(+) channels: SCNN1A/ENAC and SCN5A, K(+) channels: KCNA3/KV1.3, KCNE1, KCNQ1 and KCNH2/HERG, epithelial Ca(2+) channels: TRPV5 and TRPV6, chloride channel: BSND, creatine transporter: SLC6A8, Na(+)/dicarboxylate cotransporter: SLC13A2/NADC1, Na(+)-dependent phosphate cotransporter: SLC34A2/NAPI-2B, amino acid transporters: SLC1A5/ASCT2 and SLC6A19, glutamate transporters: SLC1A3/EAAT1, SLC1A6/EAAT4 and SLC1A7/EAAT5, glutamate receptors: GRIA1/GLUR1 and GRIK2/GLUR6, Na(+)/H(+) exchanger: SLC9A3/NHE3, and the Na(+)/K(+) ATPase. Plays a role in the regulation of renal tubular phosphate transport and bone density. Phosphorylates NEDD4L and GSK3B. Positively regulates ER transcription activity through phosphorylation of FLII. Negatively regulates the function of ITCH/AIP4 via its phosphorylation and thereby prevents CXCR4 from being efficiently sorted to lysosomes. {ECO:0000269|PubMed:12054501, ECO:0000269|PubMed:12397388, ECO:0000269|PubMed:12590200, ECO:0000269|PubMed:12632189, ECO:0000269|PubMed:12634932, ECO:0000269|PubMed:12650886, ECO:0000269|PubMed:12911626, ECO:0000269|PubMed:14706641, ECO:0000269|PubMed:15040001, ECO:0000269|PubMed:15044175, ECO:0000269|PubMed:15319523, ECO:0000269|PubMed:15496163, ECO:0000269|PubMed:15737648, ECO:0000269|PubMed:15845389, ECO:0000269|PubMed:16036218, ECO:0000269|PubMed:16888620, ECO:0000269|PubMed:17167223, ECO:0000269|PubMed:18005662, ECO:0000269|PubMed:19293151, ECO:0000269|PubMed:20511718, ECO:0000269|PubMed:21865597}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);PI3K-Akt Signaling Pathway;Insulin Signaling;Stimuli-sensing channels;Ion channel transport;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- loftool
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.254
- hipred
- N
- hipred_score
- 0.322
- ghis
- 0.486
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Mouse Genome Informatics
- Gene name
- Sgk3
- Phenotype
- immune system 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
- regulation of cell growth;protein phosphorylation;peptidyl-serine phosphorylation;regulation of cell migration;ion transmembrane transport;intracellular signal transduction;regulation of cell population proliferation;regulation of DNA-binding transcription factor activity;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- early endosome;cytosol;recycling endosome
- Molecular function
- protein kinase activity;protein serine/threonine kinase activity;calcium channel regulator activity;protein binding;ATP binding;potassium channel regulator activity;sodium channel regulator activity;chloride channel regulator activity;phosphatidylinositol binding