KCNAB1
potassium voltage-gated channel subfamily A regulatory beta subunit 1, the group of Potassium voltage-gated channel regulatory subunits|Aldo-keto reductases
Basic information
Region (hg38): 3:156037701-156538756
Links
Phenotypes
GenCC
Source:
No genCC data.
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 KCNAB1 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 | 2 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 4 |
Variants in KCNAB1
This is a list of pathogenic ClinVar variants found in the KCNAB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-156120696-G-C | Benign (Dec 31, 2019) | |||
| 3-156120699-G-C | Benign (Dec 31, 2019) | |||
| 3-156120712-C-G | Likely benign (Dec 31, 2019) | |||
| 3-156120848-C-T | Benign (Dec 31, 2019) | |||
| 3-156457477-G-T | not specified | Uncertain significance (Jun 02, 2024) | ||
| 3-156457483-G-C | not specified | Uncertain significance (Mar 14, 2023) | ||
| 3-156474809-C-G | not specified | Uncertain significance (May 25, 2022) | ||
| 3-156516319-A-G | Benign (Dec 31, 2019) | |||
| 3-156516326-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 3-156523849-G-A | not specified | Uncertain significance (Sep 26, 2023) | ||
| 3-156523854-G-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 3-156531463-C-G | not specified | Uncertain significance (Jul 21, 2021) | ||
| 3-156531465-G-C | not specified | Uncertain significance (Jun 16, 2024) | ||
| 3-156536725-G-C | not specified | Uncertain significance (Apr 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KCNAB1 | protein_coding | protein_coding | ENST00000490337 | 14 | 501056 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0423 | 0.958 | 125705 | 0 | 43 | 125748 | 0.000171 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.15 | 142 | 235 | 0.605 | 0.0000126 | 2706 |
| Missense in Polyphen | 31 | 79.311 | 0.39087 | 954 | ||
| Synonymous | 0.590 | 82 | 89.1 | 0.921 | 0.00000528 | 806 |
| Loss of Function | 3.56 | 8 | 28.5 | 0.281 | 0.00000135 | 326 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000293 | 0.000293 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000274 | 0.000273 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytoplasmic potassium channel subunit that modulates the characteristics of the channel-forming alpha-subunits (PubMed:7499366, PubMed:7603988, PubMed:17156368,PubMed:17540341, PubMed:19713757). Modulates action potentials via its effect on the pore-forming alpha subunits (By similarity). Promotes expression of the pore-forming alpha subunits at the cell membrane, and thereby increases channel activity (By similarity). Mediates closure of delayed rectifier potassium channels by physically obstructing the pore via its N-terminal domain and increases the speed of channel closure for other family members (PubMed:9763623). Promotes the closure of KCNA1, KCNA2 and KCNA5 channels (PubMed:7499366, PubMed:7890032, PubMed:7603988, PubMed:7649300, PubMed:8938711, PubMed:12077175, PubMed:12130714, PubMed:15361858, PubMed:17540341, PubMed:19713757). Accelerates KCNA4 channel closure (PubMed:7890032, PubMed:7649300, PubMed:7890764, PubMed:9763623). Accelerates the closure of heteromeric channels formed by KCNA1 and KCNA4 (PubMed:17156368). Accelerates the closure of heteromeric channels formed by KCNA2, KCNA5 and KCNA6 (By similarity). Isoform KvB1.2 has no effect on KCNA1, KCNA2 or KCNB1 (PubMed:7890032, PubMed:7890764). Enhances KCNB1 and KCNB2 channel activity (By similarity). Binds NADPH; this is required for efficient down-regulation of potassium channel activity (PubMed:17540341). Has NADPH-dependent aldoketoreductase activity (By similarity). Oxidation of the bound NADPH strongly decreases N-type inactivation of potassium channel activity (By similarity). {ECO:0000250|UniProtKB:P63143, ECO:0000250|UniProtKB:P63144, ECO:0000269|PubMed:12077175, ECO:0000269|PubMed:12130714, ECO:0000269|PubMed:15361858, ECO:0000269|PubMed:17156368, ECO:0000269|PubMed:17540341, ECO:0000269|PubMed:19713757, ECO:0000269|PubMed:7499366, ECO:0000269|PubMed:7603988, ECO:0000269|PubMed:7649300, ECO:0000269|PubMed:7890032, ECO:0000269|PubMed:7890764, ECO:0000269|PubMed:8938711, ECO:0000269|PubMed:9763623, ECO:0000305}.;
- Pathway
- Metapathway biotransformation Phase I and II;Neuronal System;Voltage gated Potassium channels;Potassium Channels
(Consensus)
Recessive Scores
- pRec
- 0.162
Intolerance Scores
- loftool
- 0.709
- rvis_EVS
- -0.44
- rvis_percentile_EVS
- 24.46
Haploinsufficiency Scores
- pHI
- 0.799
- hipred
- Y
- hipred_score
- 0.562
- ghis
- 0.532
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.432
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kcnab1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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);
Gene ontology
- Biological process
- potassium ion transport;brain development;heart development;skeletal muscle tissue development;learning or memory;myoblast differentiation;oxidation-reduction process;diaphragm development;potassium ion transmembrane transport;regulation of potassium ion transmembrane transport;regulation of delayed rectifier potassium channel activity;negative regulation of delayed rectifier potassium channel activity;negative regulation of voltage-gated potassium channel activity
- Cellular component
- cytosol;plasma membrane;voltage-gated potassium channel complex;extrinsic component of cytoplasmic side of plasma membrane;dendrite cytoplasm;potassium channel complex;perikaryon;juxtaparanode region of axon;proximal dendrite
- Molecular function
- aldo-keto reductase (NADP) activity;voltage-gated potassium channel activity;potassium channel regulator activity;protein domain specific binding;ion channel binding;NADPH binding