BSND

barttin CLCNK type accessory subunit beta, the group of Chloride voltage-gated channels

Basic information

Region (hg38): 1:54998933-55017172

Previous symbols: [ "DFNB73" ]

Links

ENSG00000162399 ∙ NCBI:7809 ∙ OMIM:606412 ∙ HGNC:16512 ∙ Uniprot:Q8WZ55 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Bartter disease type 4A (Strong), mode of inheritance: AR
• Bartter disease type 4A (Definitive), mode of inheritance: AR
• Bartter syndrome type 4 (Supportive), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• Bartter disease type 4A (Strong), mode of inheritance: AR
• Bartter disease type 4A (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bartter syndrome, type 4A, neonatal, with sensorineural deafness	AR	Audiologic/Otolaryngologic; Renal	Individuals may have renal perturbations, (eg, including metabolic alkalosis and hypokalemia), for which treatment can be beneficial; Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Renal	11687798; 12574213; 19646679; 21158220; 21269598; 23110775; 30174009; 31667618

ClinVar

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

• not provided (19 variants)
• Bartter disease type 4A (5 variants)
• Bartter syndrome (2 variants)
• Sensorineural deafness with mild renal dysfunction (1 variants)
• Hearing impairment (1 variants)
• BSND-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BSND 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				133	3	136
missense	3	2	67	4		76
nonsense	9		4			13
start loss	1	1	1			3
frameshift	6		3			9
inframe indel			1			1
splice donor/acceptor (+/-2bp)		5				5
splice region				9		9
non coding			5	36	18	59
Total	19	8	81	173	21

Highest pathogenic variant AF is 0.000151

Variants in BSND

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

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

Position	Type	Phenotype	Significance	ClinVar
1-54998946-G-A		Bartter disease type 4A	Benign (Nov 10, 2018)
1-54998989-G-A			Likely benign (Apr 12, 2019)
1-54999012-C-T		Bartter disease type 4A	Uncertain significance (Jan 13, 2018)
1-54999031-G-C		Bartter disease type 4A	Benign (Jan 13, 2018)
1-54999070-T-C		Bartter disease type 4A	Benign (Jul 10, 2021)
1-54999117-C-G		Bartter disease type 4A	Benign (Jul 10, 2021)
1-54999143-C-T			Likely benign (Jul 03, 2018)
1-54999142-C-CCCCCTCTCCCGGGGGTGTGCAGGCCAGGGACTGGCCAGGCAG		not specified	Uncertain significance (Jul 19, 2023)
1-54999153-G-A		Bartter disease type 4A	Uncertain significance (Jan 13, 2018)
1-54999162-C-T		Bartter disease type 4A • not specified	Benign/Likely benign (Jan 12, 2018)
1-54999187-A-T		Bartter disease type 4A	Pathogenic (Sep 05, 2022)
1-54999189-G-A		Bartter disease type 4A • Bartter syndrome	Pathogenic/Likely pathogenic (Jan 02, 2024)
1-54999195-C-T		Bartter syndrome • Bartter disease type 4A • not specified	Likely benign (Dec 14, 2023)
1-54999196-G-A		not specified • Bartter disease type 4A • Bartter syndrome	Uncertain significance (Feb 17, 2023)
1-54999196-G-T		Sensorineural deafness with mild renal dysfunction • Hearing impairment • Bartter disease type 4A	Pathogenic (Oct 17, 2023)
1-54999202-A-G		Bartter disease type 4A • Bartter syndrome • BSND-related disorder	Conflicting classifications of pathogenicity (Jan 31, 2024)
1-54999208-C-G			Pathogenic (Nov 10, 2022)
1-54999208-C-T		Bartter disease type 4A • Bartter syndrome	Pathogenic/Likely pathogenic (Nov 10, 2023)
1-54999209-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-54999209-G-T		Bartter disease type 4A	Pathogenic (Nov 01, 2001)
1-54999210-G-A			Likely benign (Jan 24, 2023)
1-54999210-G-T			Likely benign (Dec 23, 2022)
1-54999213-C-T		Bartter syndrome	Likely benign (Jan 14, 2024)
1-54999214-G-A		Bartter disease type 4A • Bartter syndrome	Pathogenic/Likely pathogenic (Feb 26, 2024)
1-54999216-C-T			Likely benign (Mar 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BSND	protein_coding	protein_coding	ENST00000371265	4	11951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-10	0.0256	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0663	190	193	0.987	0.0000112	2125
Missense in Polyphen		72	70.195	1.0257		796
Synonymous	-1.42	96	79.8	1.20	0.00000501	615
Loss of Function	-0.605	14	11.8	1.19	5.06e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00227
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.0000544	0.0000544
South Asian	0.000490	0.000490
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a beta-subunit for CLCNKA and CLCNKB chloride channels. In the kidney CLCNK/BSND heteromers mediate chloride reabsorption by facilitating its basolateral efflux. In the stria, CLCNK/BSND channels drive potassium secretion by recycling chloride for the basolateral SLC12A2 cotransporter. {ECO:0000269|PubMed:11734858, ECO:0000269|PubMed:12111250}.
• Disease: DISEASE: Bartter syndrome 4A, neonatal, with sensorineural deafness (BARTS4A) [MIM:602522]: A form of Bartter syndrome, an autosomal recessive disorder characterized by impaired salt reabsorption in the thick ascending loop of Henle with pronounced salt wasting, hypokalemic metabolic alkalosis, and varying degrees of hypercalciuria. BARTS4A is associated with sensorineural deafness. {ECO:0000269|PubMed:11687798, ECO:0000269|PubMed:12111250, ECO:0000269|PubMed:12574213, ECO:0000269|PubMed:12761627}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Diuretics Pathway, Pharmacodynamics;Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.365

Intolerance Scores

• loftool: 0.323
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.0748
• hipred: N
• hipred_score: 0.123
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0856

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bsnd
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ion transmembrane transport;chloride transmembrane transport
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;basolateral plasma membrane;protein-containing complex
• Molecular function: voltage-gated chloride channel activity;chloride channel activity;chloride channel regulator activity