SLC8B1

solute carrier family 8 member B1, the group of Solute carrier family 8

Basic information

Region (hg38): 12:113298759-113359493

Previous symbols: [ "SLC24A6" ]

Links

ENSG00000089060 ∙ NCBI:80024 ∙ OMIM:609841 ∙ HGNC:26175 ∙ Uniprot:Q6J4K2 ∙ 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 SLC8B1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC8B1 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						0
missense			56	1		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	1	0

Variants in SLC8B1

This is a list of pathogenic ClinVar variants found in the SLC8B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113299824-C-T		not specified	Uncertain significance (Oct 24, 2024)
12-113299829-A-G		not specified	Uncertain significance (Nov 10, 2024)
12-113299869-C-T		not specified	Uncertain significance (May 20, 2024)
12-113299892-A-C		not specified	Uncertain significance (Aug 20, 2024)
12-113299935-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-113299940-G-C		not specified	Uncertain significance (May 30, 2024)
12-113299962-C-T		not specified	Uncertain significance (Nov 01, 2022)
12-113304340-C-G		not specified	Uncertain significance (Aug 26, 2022)
12-113304340-C-T		not specified	Uncertain significance (Sep 12, 2023)
12-113304365-G-C		not specified	Uncertain significance (Feb 15, 2023)
12-113304377-C-A		not specified	Uncertain significance (Feb 15, 2025)
12-113304377-C-G		not specified	Uncertain significance (Oct 05, 2022)
12-113304377-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-113306533-C-T		not specified	Uncertain significance (Oct 14, 2023)
12-113306548-C-T		not specified	Uncertain significance (Feb 13, 2025)
12-113306559-G-C		not specified	Uncertain significance (Jun 25, 2024)
12-113307747-C-G		not specified	Uncertain significance (Apr 11, 2023)
12-113307793-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-113307799-C-T		not specified	Uncertain significance (Feb 22, 2025)
12-113307817-T-C		not specified	Uncertain significance (Nov 21, 2024)
12-113310248-G-A		not specified	Uncertain significance (Jan 01, 2025)
12-113310257-T-G		not specified	Uncertain significance (Feb 08, 2025)
12-113310263-A-G		not specified	Uncertain significance (Jul 10, 2024)
12-113310290-A-T		not specified	Uncertain significance (Dec 11, 2024)
12-113310314-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC8B1	protein_coding	protein_coding	ENST00000552014	15	60735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.03e-16	0.0280	125500	1	247	125748	0.000987

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.318	326	343	0.952	0.0000208	3717
Missense in Polyphen		102	114.34	0.89209		1280
Synonymous	-0.0153	152	152	1.00	0.00000940	1283
Loss of Function	0.539	26	29.1	0.892	0.00000152	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000402	0.000387
Ashkenazi Jewish	0.00828	0.00817
East Asian	0.000217	0.000217
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000593	0.000589
Middle Eastern	0.000217	0.000217
South Asian	0.00232	0.00232
Other	0.00164	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial sodium/calcium antiporter that mediates sodium-dependent calcium efflux from mitochondrion, by mediating the exchange of 3 sodium ions per 1 calcium ion (PubMed:20018762, PubMed:22829870, PubMed:23056385, PubMed:24898248, PubMed:28219928). Plays a central role in mitochondrial calcium homeostasis by mediating mitochondrial calcium extrusion: calcium efflux is essential for mitochondrial function and cell survival, notably in cardiomyocytes (By similarity). Regulates rates of glucose-dependent insulin secretion in pancreatic beta-cells during the first phase of insulin secretion: acts by mediating efflux of calcium from mitochondrion, thereby affecting cytoplasmic calcium responses (PubMed:23056385). Required for store-operated Ca(2+) entry (SOCE) and Ca(2+) release-activated Ca(2+) (CRAC) channel regulation: sodium transport by SLC8B1 leads to promote calcium-shuttling that modulates mitochondrial redox status, thereby regulating SOCE activity (PubMed:28219928). Involved in B-lymphocyte chemotaxis (By similarity). Able to transport Ca(2+) in exchange of either Li(+) or Na(+), explaining how Li(+) catalyzes Ca(2+) exchange (PubMed:15060069). In contrast to other members of the family its function is independent of K(+) (PubMed:15060069). {ECO:0000250|UniProtKB:Q925Q3, ECO:0000269|PubMed:15060069, ECO:0000269|PubMed:20018762, ECO:0000269|PubMed:22829870, ECO:0000269|PubMed:23056385, ECO:0000269|PubMed:24898248, ECO:0000269|PubMed:28219928}.
• Pathway: Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Mitochondrial calcium ion transport (Consensus)

Intolerance Scores

• rvis_EVS: -1
• rvis_percentile_EVS: 8.54

Haploinsufficiency Scores

• pHI: 0.365
• hipred: N
• hipred_score: 0.251
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc8b1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: ion transport;mitochondrial calcium ion transmembrane transport;sodium ion transmembrane transport;glucose homeostasis;regulation of insulin secretion;response to stimulus;regulation of cytosolic calcium ion concentration;mitochondrial calcium ion homeostasis;regulation of cardiac muscle cell membrane potential;calcium export from the mitochondrion;regulation of lymphocyte chemotaxis;regulation of store-operated calcium entry
• Cellular component: mitochondrial inner membrane;plasma membrane;mitochondrial crista;integral component of mitochondrial membrane;sarcolemma
• Molecular function: calcium:sodium antiporter activity;calcium:cation antiporter activity;protein homodimerization activity;calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential