GeneBe

SCNN1D

protein-coding

sodium channel epithelial 1 subunit delta, the group of Sodium channels epithelial

Gene summary

Contributes to sodium channel activity. Involved in cellular response to acidic pH; intracellular sodium ion homeostasis; and sodium ion import across plasma membrane. Located in actin cytoskeleton and membrane. Part of sodium channel complex. Is active in apical plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001130413.4

Inheritance

—

ClinVar variants

U:204B:43

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.24

Max pathogenic AF

—

Genomic locus

chr1:1,280,436-1,292,029

External References & Databases

Ensembl (ENSG00000162572)NCBI Gene (6339)OMIM (601328)HGNC:10601GenCCUniProt (P51172)AlphaFoldClinVar (SCNN1D)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~11.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCNN1D variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 221
not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130413.4. 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
4
clinvar
9
clinvar
 13
missense
198
clinvar
34
clinvar
 232
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total00204430247
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001130413.4RefSeqNP_001123885.218MANE Select
ENST00000379116.10EnsemblENSP00000368411.518MANE Select
ENST00000325425.12EnsemblENSP00000321594.815Standard
ENST00000325425.13EnsemblENSP00000321594.815Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Polythiazide Action Pathway
  • Methyclothiazide Action Pathway
  • Bumetanide Action Pathway
  • Spironolactone Action Pathway
  • Eplerenone Action Pathway

Biological Process

  • sodium ion transport
  • sodium ion transmembrane transport
  • response to stimulus
  • sensory perception of taste

Molecular Function

  • protein binding
  • ligand-gated sodium channel activity

Cellular Component

  • plasma membrane
  • actin cytoskeleton
  • membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000379116
Coding exons
18
Length
11594
Individuals with no LoFs
124639
Homozygous LoFs
1
Heterozygous LoFs
430
Defined
125070
p
0.00172
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.7815264781.100.00003115017
Missense (PolyPhen)10797.7681.09441154
Synonymous-3.992992231.340.00001591718
Loss of Function-1.334536.41.240.00000179404

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00340.0034notable
Latino/Admixed American0.000710.00069rare
Ashkenazi Jewish0.000510.00050rare
East Asian0.000280.00027rare
Finnish0.000200.00018rare
European (Non-Finnish)0.000860.00081rare
South Asian0.00790.0077notable
Other0.00200.0020notable

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. Controls the reabsorption of sodium in kidney, colon, lung and sweat glands. Also plays a role in taste perception. {ECO:0000269|PubMed:16423824, ECO:0000269|PubMed:7499195}.;

Recessive Scores

pRec
0.140

Intolerance Scores

LoFtool
0.840
RVIS EVS
1.77
RVIS percentile EVS
96.78

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.825

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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