KCNIP3
potassium voltage-gated channel interacting protein 3, the group of EF-hand domain containing|Potassium voltage-gated channel regulatory subunits
Basic information
Region (hg38): 2:95297327-95386077
Previous symbols: [ "CSEN" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNIP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013434.5. 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 | 41 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KCNIP3 | protein_coding | protein_coding | ENST00000295225 | 9 | 88774 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0376 | 0.956 | 125722 | 0 | 10 | 125732 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.888 | 126 | 157 | 0.801 | 0.00000943 | 1708 |
| Missense in Polyphen | 49 | 58.641 | 0.8356 | 688 | ||
| Synonymous | -0.538 | 75 | 69.3 | 1.08 | 0.00000499 | 470 |
| Loss of Function | 2.38 | 5 | 14.9 | 0.335 | 6.35e-7 | 176 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000311 | 0.000308 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000331 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-dependent transcriptional repressor that binds to the DRE element of genes including PDYN and FOS. Affinity for DNA is reduced upon binding to calcium and enhanced by binding to magnesium. Seems to be involved in nociception (By similarity). {ECO:0000250|UniProtKB:Q9QXT8}.; FUNCTION: May play a role in the regulation of PSEN2 proteolytic processing and apoptosis. Together with PSEN2 involved in modulation of amyloid-beta formation. {ECO:0000269|PubMed:11259376, ECO:0000269|PubMed:11988022, ECO:0000269|PubMed:9771752}.;
- Pathway
- Human Thyroid Stimulating Hormone (TSH) signaling pathway;repression of pain sensation by the transcriptional regulator dream;Phase 1 - inactivation of fast Na+ channels;Cardiac conduction;Muscle contraction;IL3
(Consensus)
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- loftool
- 0.206
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.152
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.966
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kcnip3
- 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); homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- kcnip3b
- Affected structure
- endocrine pancreas
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;intracellular protein transport;apoptotic process;signal transduction;potassium ion transmembrane transport;protein localization to plasma membrane;regulation of potassium ion transmembrane transport
- Cellular component
- nucleus;endoplasmic reticulum;Golgi apparatus;cytosol;plasma membrane;voltage-gated potassium channel complex;dendrite;protein-DNA complex;axon terminus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity;voltage-gated ion channel activity;potassium channel activity;calcium ion binding;protein binding;potassium channel regulator activity;ion channel binding