SCNN1B

protein-coding

sodium 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

NM_000336.3

Inheritance

AD, SD, AR, Digenic (with CFTR or other SCCN1 genes)

ClinVar variants

P:50U:222B:93

Top phenotype

Pseudohypoaldosteronism, type IB2; Liddle syndrome 1; Bronchiectasis with or without elevated sweat chloride 1

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr16:23,278,231-23,381,294

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~103.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Liddle syndrome 1DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0020607

Submitter: Ambry Genetics

Liddle syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008323

Submitter: Orphanet

bronchiectasis with or without elevated sweat chloride 1LIMITED

Inheritance Pattern: SD

Disease ID:MONDO:0008887

Submitter: Ambry Genetics

Liddle syndrome 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0020607

Submitter: Labcorp Genetics (formerly Invitae)

pseudohypoaldosteronism, type IB1, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009917

Submitter: PanelApp Australia

pseudohypoaldosteronism, type IB1, autosomal recessiveSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009917

Submitter: Orphanet

pseudohypoaldosteronism, type IB1, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009917

Submitter: Labcorp Genetics (formerly Invitae)

Liddle syndrome 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0020607

Submitter: PanelApp Australia

pseudohypoaldosteronism, type IB2, autosomal recessiveDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0859317

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Pseudohypoaldosteronism, type IB2; Liddle syndrome 1; Bronchiectasis with or without elevated sweat chloride 1AD/AR/Digenic (with CFTR or other SCCN1 genes)

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

Refs: 7046191; 6262354; 3550146; 264740; 7954808; 8524790; 8589714; 10202170; 16207733; 18507830; 19017867; 32840096Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCNN1B variants in ClinVar

15 Conditions Cataloged
not providedTotal: 236
Liddle syndrome 1Total: 184
Bronchiectasis with or without elevated sweat chloride 1Total: 180
Pseudohypoaldosteronism, type IB2, autosomal recessiveTotal: 129
Inborn genetic diseasesTotal: 91
Pseudohypoaldosteronism, type IB1, autosomal recessiveTotal: 64
not specifiedTotal: 34
SCNN1B-related disorderTotal: 24

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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
60
clinvar
1
clinvar
68
missense
4
clinvar
11
clinvar
210
clinvar
29
clinvar
3
clinvar
257
nonsense
6
clinvar
9
clinvar
1
clinvar
16
start loss
0
frameshift
4
clinvar
10
clinvar
3
clinvar
17
splice donor/acceptor (+/-2bp)
4
clinvar
2
clinvar
1
clinvar
7
Total1832222894365

Highest pathogenic variant AF is 0.00008611034

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000336.3RefSeqNP_000327.212MANE Select
ENST00000343070.7EnsemblENSP00000345751.212MANE Select
NM_001410900.1RefSeqNP_001397829.111Standard
ENST00000307331.9EnsemblENSP00000302874.514Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2123623740.9690.00002364238
Missense (PolyPhen)114146.310.779161659
Synonymous-0.8731721581.090.00001091226
Loss of Function2.451732.00.5320.00000159356

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American00.0absent
Ashkenazi Jewish0.00110.0011notable
East Asian0.000160.00016rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000160.00016rare
South Asian0.000260.00026rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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