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GeneBe

SCNN1D

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

Basic information

Region (hg38): 1:1280435-1292029

Links

ENSG00000162572NCBI:6339OMIM:601328HGNC:10601Uniprot:P51172AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCNN1D gene.

  • Inborn genetic diseases (64 variants)
  • not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCNN1D 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
5
clinvar
5
missense
54
clinvar
12
clinvar
66
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 54 17 0

Variants in SCNN1D

This is a list of pathogenic ClinVar variants found in the SCNN1D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-1281252-C-T Inborn genetic diseases Likely benign (Apr 22, 2022)2391021
1-1281275-G-A Inborn genetic diseases Likely benign (Oct 26, 2022)2360059
1-1281287-G-A Inborn genetic diseases Uncertain significance (May 23, 2023)2512162
1-1281479-C-T Inborn genetic diseases Uncertain significance (Aug 03, 2022)2384942
1-1281490-G-A Inborn genetic diseases Likely benign (Sep 17, 2021)2412083
1-1281497-C-T Inborn genetic diseases Uncertain significance (Oct 12, 2021)2341910
1-1281523-G-A Inborn genetic diseases Uncertain significance (Dec 27, 2022)2382730
1-1281527-C-T Inborn genetic diseases Uncertain significance (Nov 09, 2021)2221482
1-1281590-C-T Inborn genetic diseases Likely benign (Aug 02, 2021)2241017
1-1281608-C-A Inborn genetic diseases Uncertain significance (Sep 17, 2021)2251745
1-1283978-G-A Inborn genetic diseases Uncertain significance (Nov 18, 2022)2376110
1-1284017-C-T Inborn genetic diseases Uncertain significance (May 26, 2023)2534551
1-1284044-T-C Inborn genetic diseases Uncertain significance (Nov 30, 2022)2218972
1-1284063-A-G Inborn genetic diseases Uncertain significance (Mar 29, 2022)2280131
1-1284071-G-T Inborn genetic diseases Uncertain significance (Jun 23, 2021)2393662
1-1285631-C-A Likely benign (Nov 01, 2023)2672317
1-1285939-C-T Inborn genetic diseases Uncertain significance (Nov 23, 2021)2226825
1-1285963-C-T Inborn genetic diseases Uncertain significance (Oct 03, 2022)2393955
1-1286028-C-T Inborn genetic diseases Uncertain significance (Sep 13, 2023)2591936
1-1286044-T-C Inborn genetic diseases Uncertain significance (Oct 12, 2021)2254787
1-1286079-C-T Inborn genetic diseases Uncertain significance (Nov 30, 2022)2398207
1-1286084-G-A Likely benign (Nov 01, 2022)2637991
1-1286103-C-T Inborn genetic diseases Uncertain significance (Apr 18, 2023)1330448
1-1286151-G-A Inborn genetic diseases Likely benign (Jan 26, 2022)2348687
1-1286185-G-A Inborn genetic diseases Likely benign (Feb 10, 2022)2404667

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCNN1Dprotein_codingprotein_codingENST00000379116 1811594
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.65e-336.18e-712463914301250700.00172
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.7815264781.100.00003115017
Missense in Polyphen10797.7681.09441154
Synonymous-3.992992231.340.00001591718
Loss of Function-1.334536.41.240.00000179404

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004090.00407
Ashkenazi Jewish0.0005150.000499
East Asian0.0002790.000272
Finnish0.0001980.000185
European (Non-Finnish)0.0008560.000808
Middle Eastern0.0002790.000272
South Asian0.007900.00774
Other0.002040.00197

dbNSFP

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}.;
Pathway
Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Ethacrynic Acid Action Pathway;Quinethazone Action Pathway;Bendroflumethiazide Action Pathway;Chlorthalidone Action Pathway;Trichlormethiazide Action Pathway;Iminoglycinuria;Lysinuric Protein Intolerance;Blue diaper syndrome;Lysinuric protein intolerance (LPI);Cystinuria;Indapamide Action Pathway;Furosemide Action Pathway;Torsemide Action Pathway;Hartnup Disorder;Glucose Transporter Defect (SGLT2);Kidney Function;Glucose Transporter Defect (SGLT2);Metolazone Action Pathway;Hydrochlorothiazide Action Pathway;Cyclothiazide Action Pathway;Hydroflumethiazide Action Pathway;Chlorothiazide Action Pathway;Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

pRec
0.140

Intolerance Scores

loftool
0.840
rvis_EVS
1.77
rvis_percentile_EVS
96.78

Haploinsufficiency Scores

pHI
0.700
hipred
N
hipred_score
0.341
ghis
0.419

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.825

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
sodium ion transport;sodium ion transmembrane transport;response to stimulus;sensory perception of taste
Cellular component
plasma membrane;actin cytoskeleton;membrane;integral component of membrane
Molecular function
protein binding;ligand-gated sodium channel activity