SCNN1B
protein-codingsodium channel epithelial 1 subunit beta, the group of Sodium channels epithelial
Gene summary
Nonvoltage-gated, amiloride-sensitive, sodium channels control fluid and electrolyte transport across epithelia in many organs. These channels are heteromeric complexes consisting of 3 subunits: alpha, beta, and gamma. This gene encodes the beta subunit, and mutations in this gene have been associated with pseudohypoaldosteronism type 1 (PHA1), and Liddle syndrome. [provided by RefSeq, Apr 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~103.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0020607
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0008323
Submitter: Orphanet
Inheritance Pattern: SD
Disease ID:MONDO:0008887
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0020607
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009917
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009917
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009917
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0020607
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0859317
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Pulmonary; Renal
Intervention: Allergy/Immunology/Infectious; Pulmonary; Renal
Rationale: In Pseudohypoaldosteronism, type IB2, treatment with electrolyte replacement and control of hyperkalemia can be effective; In Liddle syndrome, certain medications (eg, amiloride, triamterene, but not spironolactone) and dietary sodium restriction can effectively treat hypertension and hypokalemia; In Bronchiectasis with or without elevated sweat chloride 1, as in cystic fibrosis, early and aggressive pulmonary and other management (eg, related to prophylaxis and management of respiratory infections) may decrease morbidity
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SCNN1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000336.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 60 | 1 | 68 | ||
| missense | 4 | 11 | 210 | 29 | 3 | 257 |
| nonsense | 6 | 9 | 1 | 16 | ||
| start loss | 0 | |||||
| frameshift | 4 | 10 | 3 | 17 | ||
| splice donor/acceptor (+/-2bp) | 4 | 2 | 1 | 7 | ||
| Total | 18 | 32 | 222 | 89 | 4 | 365 |
Highest pathogenic variant AF is 0.00008611034
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000327.2 | 12 | MANE Select | |
| Ensembl | ENSP00000345751.2 | 12 | MANE Select | |
| RefSeq | NP_001397829.1 | 11 | Standard | |
| Ensembl | ENSP00000302874.5 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Aldosterone-regulated sodium reabsorption - Homo sapiens (human)
- Taste transduction - Homo sapiens (human)
- Diuretics Pathway, Pharmacodynamics
- Polythiazide Action Pathway
- Methyclothiazide Action Pathway
Biological Process
- sodium ion transport
- excretion
- sodium ion transmembrane transport
- multicellular organismal water homeostasis
- response to stimulus
Molecular Function
- protein binding
- ligand-gated sodium channel activity
- WW domain binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- apical plasma membrane
- cytoplasmic vesicle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000343070
- Coding exons
- 12
- Length
- 103069
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 125748
- p
- 0.000187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.212 | 362 | 374 | 0.969 | 0.0000236 | 4238 |
| Missense (PolyPhen) | 114 | 146.31 | 0.77916 | 1659 | ||
| Synonymous | -0.873 | 172 | 158 | 1.09 | 0.0000109 | 1226 |
| Loss of Function | 2.45 | 17 | 32.0 | 0.532 | 0.00000159 | 356 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.0011 | 0.0011 | notable |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sodium permeable non-voltage-sensitive ion channel inhibited by the diuretic amiloride. Mediates the electrodiffusion of the luminal sodium (and water, which follows osmotically) through the apical membrane of epithelial cells. Plays an essential role in electrolyte and blood pressure homeostasis, but also in airway surface liquid homeostasis, which is important for proper clearance of mucus. Controls the reabsorption of sodium in kidney, colon, lung and sweat glands. Also plays a role in taste perception. {ECO:0000269|PubMed:7762608, ECO:0000303|PubMed:7490094}.;
- Disease
- DISEASE: Pseudohypoaldosteronism 1, autosomal recessive (PHA1B) [MIM:264350]: A rare salt wasting disease resulting from target organ unresponsiveness to mineralocorticoids. PHA1B is a severe form involving multiple organ systems, and characterized by an often fulminant presentation in the neonatal period with dehydration, hyponatremia, hyperkalemia, metabolic acidosis, failure to thrive and weight loss. {ECO:0000269|PubMed:8589714}. Note=The disease is caused by mutations affecting the gene represented in this entry. The degree of channel function impairment differentially affects the renin-aldosterone system and urinary Na/K ratios, resulting in distinct genotype-phenotype relationships in PHA1 patients. Loss-of-function mutations are associated with a severe clinical course and age-dependent hyperactivation of the renin-aldosterone system. This feature is not observed in patients with missense mutations that reduce but do not eliminate channel function. Markedly reduced channel activity results in impaired linear growth and delayed puberty (PubMed:18634878). {ECO:0000269|PubMed:18634878}.; DISEASE: Liddle syndrome (LIDLS) [MIM:177200]: An autosomal dominant disorder characterized by hypertension, hypokalemic alkalosis, and suppression of plasma renin activity and aldosterone secretion. {ECO:0000269|PubMed:15483078, ECO:0000269|PubMed:7550319, ECO:0000269|PubMed:8524790, ECO:0000269|PubMed:8601645, ECO:0000269|PubMed:9626162, ECO:0000269|PubMed:9794716}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bronchiectasis with or without elevated sweat chloride 1 (BESC1) [MIM:211400]: A debilitating respiratory disease characterized by chronic, abnormal dilatation of the bronchi and other cystic fibrosis-like symptoms in the absence of known causes of bronchiectasis (cystic fibrosis, autoimmune diseases, ciliary dyskinesia, common variable immunodeficiency, foreign body obstruction). Clinical features include sub-normal lung function, sinopulmonary infections, chronic productive cough, excessive sputum production, and elevated sweat chloride in some cases. {ECO:0000269|PubMed:16207733, ECO:0000269|PubMed:18507830, ECO:0000269|PubMed:19017867}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.269
Intolerance Scores
- LoFtool
- 0.552
- RVIS EVS
- 0.16
- RVIS percentile EVS
- 64.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.721
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |