SLC24A3

solute carrier family 24 member 3, the group of Solute carrier family 24

Basic information

Region (hg38): 20:19212641-19722926

Links

ENSG00000185052 ∙ NCBI:57419 ∙ OMIM:609839 ∙ HGNC:10977 ∙ Uniprot:Q9HC58 ∙ 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 SLC24A3 gene.

• Inborn genetic diseases (28 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC24A3 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				1		1
missense			29			29
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	29	1	0

Variants in SLC24A3

This is a list of pathogenic ClinVar variants found in the SLC24A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-19212849-C-A		not specified	Uncertain significance (Sep 14, 2023)
20-19212850-C-T		not specified	Uncertain significance (Apr 07, 2022)
20-19212859-A-C		not specified	Uncertain significance (Aug 04, 2021)
20-19212861-G-C		not specified	Uncertain significance (Dec 28, 2023)
20-19212871-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2021)
20-19212886-G-A		not specified	Uncertain significance (Oct 20, 2021)
20-19212922-T-C		not specified	Uncertain significance (Mar 27, 2023)
20-19281045-G-A		not specified	Uncertain significance (Jul 06, 2021)
20-19281049-A-C		not specified	Uncertain significance (Aug 11, 2022)
20-19281061-G-A		not specified	Uncertain significance (Jul 05, 2023)
20-19281071-G-C		not specified	Uncertain significance (Jul 20, 2021)
20-19515494-A-T		not specified	Uncertain significance (Jan 27, 2022)
20-19515523-G-A		not specified	Uncertain significance (Jun 16, 2023)
20-19584972-G-A		not specified	Uncertain significance (Aug 29, 2022)
20-19585470-G-C		not specified	Uncertain significance (Nov 16, 2022)
20-19654115-G-C			Likely benign (Jun 21, 2018)
20-19673632-C-G			Likely benign (Apr 01, 2024)
20-19673636-T-C		not specified	Uncertain significance (Aug 14, 2023)
20-19673652-G-A		not specified	Uncertain significance (May 09, 2023)
20-19681904-G-T		not specified	Uncertain significance (Apr 25, 2023)
20-19681907-G-A		not specified	Uncertain significance (Feb 16, 2023)
20-19681916-G-A		not specified	Uncertain significance (Aug 01, 2023)
20-19681922-G-A		not specified	Uncertain significance (Nov 03, 2022)
20-19681964-G-A		not specified	Uncertain significance (Sep 23, 2023)
20-19684301-C-T		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC24A3	protein_coding	protein_coding	ENST00000328041	17	510292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.879	0.121	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	264	378	0.698	0.0000218	4219
Missense in Polyphen		64	148.87	0.4299		1633
Synonymous	0.0809	160	161	0.992	0.0000113	1252
Loss of Function	4.39	6	33.3	0.180	0.00000158	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000374	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+). {ECO:0000250}.
• Pathway: Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.308
• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.3

Haploinsufficiency Scores

• pHI: 0.190
• hipred: Y
• hipred_score: 0.728
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc24a3

Gene ontology

• Biological process: ion transport;potassium ion transport;cellular calcium ion homeostasis;sodium ion transmembrane transport;calcium ion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: calcium channel activity;calcium, potassium:sodium antiporter activity;symporter activity