SCNN1D

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

Basic information

Region (hg38): 1:1280435-1292029

Links

ENSG00000162572 ∙ NCBI:6339 ∙ OMIM:601328 ∙ HGNC:10601 ∙ Uniprot:P51172 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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		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)
1-1281479-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 (Nov 09, 2021)
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 (Nov 18, 2022)
1-1284017-C-T		not specified	Uncertain significance (May 26, 2023)
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)
1-1285631-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)
1-1285963-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-1286028-C-T		not specified	Uncertain significance (Sep 13, 2023)
1-1286044-T-C		not specified	Uncertain significance (Oct 12, 2021)
1-1286079-C-T		not specified	Uncertain significance (Nov 30, 2022)
1-1286084-G-A			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

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: 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

	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