SCNN1D
Basic information
Region (hg38): 1:1280436-1292029
Links
Phenotypes
GenCC
Source:
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 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 | |||||
missense | 70 | 18 | 88 | |||
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 | 70 | 23 | 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 | not specified | Likely benign (Apr 22, 2022) | ||
1-1281273-C-G | not specified | Uncertain significance (Jan 04, 2024) | ||
1-1281275-G-A | not specified | Likely benign (Oct 26, 2022) | ||
1-1281287-G-A | not specified | Uncertain significance (May 23, 2023) | ||
1-1281455-G-A | not specified | Likely benign (Apr 29, 2024) | ||
1-1281479-C-T | not specified | Uncertain significance (Aug 03, 2022) | ||
1-1281490-G-A | not specified | Likely benign (Sep 17, 2021) | ||
1-1281497-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
1-1281523-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
1-1281527-C-T | not specified | Uncertain significance (Oct 29, 2024) | ||
1-1281554-T-C | not specified | Uncertain significance (Dec 06, 2024) | ||
1-1281580-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
1-1281590-C-T | not specified | Likely benign (Aug 02, 2021) | ||
1-1281608-C-A | not specified | Uncertain significance (Sep 17, 2021) | ||
1-1282278-C-T | not specified | Uncertain significance (Dec 26, 2023) | ||
1-1283978-G-A | not specified | Uncertain significance (Dec 04, 2024) | ||
1-1284017-C-T | not specified | Uncertain significance (May 26, 2023) | ||
1-1284021-C-T | not specified | Uncertain significance (May 28, 2024) | ||
1-1284044-T-C | not specified | Uncertain significance (Nov 30, 2022) | ||
1-1284063-A-G | not specified | Uncertain significance (Mar 29, 2022) | ||
1-1284071-G-T | not specified | Uncertain significance (Jun 23, 2021) | ||
1-1285573-C-T | not specified | Uncertain significance (Apr 27, 2024) | ||
1-1285631-C-A | Likely benign (Nov 01, 2023) | |||
1-1285644-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
1-1285939-C-T | not specified | Uncertain significance (Nov 23, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SCNN1D | protein_coding | protein_coding | ENST00000379116 | 18 | 11594 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.65e-33 | 6.18e-7 | 124639 | 1 | 430 | 125070 | 0.00172 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.781 | 526 | 478 | 1.10 | 0.0000311 | 5017 |
Missense in Polyphen | 107 | 97.768 | 1.0944 | 1154 | ||
Synonymous | -3.99 | 299 | 223 | 1.34 | 0.0000159 | 1718 |
Loss of Function | -1.33 | 45 | 36.4 | 1.24 | 0.00000179 | 404 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00409 | 0.00407 |
Ashkenazi Jewish | 0.000515 | 0.000499 |
East Asian | 0.000279 | 0.000272 |
Finnish | 0.000198 | 0.000185 |
European (Non-Finnish) | 0.000856 | 0.000808 |
Middle Eastern | 0.000279 | 0.000272 |
South Asian | 0.00790 | 0.00774 |
Other | 0.00204 | 0.00197 |
dbNSFP
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. 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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