SLC8A2

solute carrier family 8 member A2, the group of Solute carrier family 8

Basic information

Region (hg38): 19:47428017-47471893

Links

ENSG00000118160 ∙ NCBI:6543 ∙ OMIM:601901 ∙ HGNC:11069 ∙ Uniprot:Q9UPR5 ∙ 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 SLC8A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC8A2 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				7	1	8
missense			30	1		31
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	30	8	1

Variants in SLC8A2

This is a list of pathogenic ClinVar variants found in the SLC8A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47430209-G-A			Likely benign (Oct 01, 2023)
19-47430219-G-C		not specified	Uncertain significance (Mar 19, 2024)
19-47430316-G-C		not specified	Uncertain significance (Sep 06, 2022)
19-47430431-G-C		not specified	Uncertain significance (Dec 13, 2022)
19-47430471-A-G			Benign (Apr 26, 2021)
19-47432259-A-G		not specified	Uncertain significance (Aug 11, 2022)
19-47432267-G-A			Likely benign (Nov 01, 2022)
19-47432385-T-A		not specified	Uncertain significance (Jul 27, 2022)
19-47432440-C-T		not specified	Uncertain significance (Feb 02, 2022)
19-47437886-C-A		not specified	Uncertain significance (Jan 06, 2023)
19-47437925-A-G		not specified	Uncertain significance (Jun 05, 2023)
19-47437931-C-T		not specified	Uncertain significance (Jan 08, 2024)
19-47437932-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-47441355-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-47441409-C-T		not specified	Uncertain significance (Dec 17, 2023)
19-47447837-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-47448050-C-G		not specified	Uncertain significance (Mar 04, 2024)
19-47448108-G-C			Likely benign (Nov 01, 2022)
19-47448111-C-G			Likely benign (Oct 01, 2023)
19-47457006-C-G		not specified	Uncertain significance (Oct 26, 2021)
19-47457015-G-C		not specified	Uncertain significance (Aug 12, 2022)
19-47457036-C-G		not specified	Uncertain significance (Jan 09, 2024)
19-47457086-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-47457106-G-A			Likely benign (Feb 01, 2024)
19-47457125-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC8A2	protein_coding	protein_coding	ENST00000236877	9	44152

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00367	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.24	224	579	0.387	0.0000353	5898
Missense in Polyphen		49	234.98	0.20853		2308
Synonymous	1.51	236	267	0.882	0.0000191	1943
Loss of Function	4.55	3	29.8	0.101	0.00000136	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000663	0.0000462
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the electrogenic exchange of Ca(2+) against Na(+) ions across the cell membrane, and thereby contributes to the regulation of cytoplasmic Ca(2+) levels and Ca(2+)-dependent cellular processes. Contributes to cellular Ca(2+) homeostasis in excitable cells. Contributes to the rapid decrease of cytoplasmic Ca(2+) levels back to baseline after neuronal activation, and thereby contributes to modulate synaptic plasticity, learning and memory. Plays a role in regulating urinary Ca(2+) and Na(+) excretion. {ECO:0000250|UniProtKB:Q8K596}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Olfactory transduction - Homo sapiens (human);Antiarrhythmic Pathway, Pharmacodynamics;Ion homeostasis;Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Cardiac conduction;Muscle contraction;Hemostasis;Reduction of cytosolic Ca++ levels;Platelet calcium homeostasis;Platelet homeostasis (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.0166
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.317
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.451

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc8a2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: ion transport;cellular calcium ion homeostasis;cell communication;learning;memory;sodium ion transmembrane transport;regulation of short-term neuronal synaptic plasticity;long-term synaptic potentiation;calcium ion transmembrane transport;regulation of cardiac conduction
• Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane;dendritic spine;perikaryon
• Molecular function: calcium:sodium antiporter activity;calmodulin binding;metal ion binding