SLC24A3

protein-coding

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

Gene summary

Plasma membrane sodium/calcium exchangers are an important component of intracellular calcium homeostasis and electrical conduction. Potassium-dependent sodium/calcium exchangers such as SLC24A3 are believed to transport 1 intracellular calcium and 1 potassium ion in exchange for 4 extracellular sodium ions (Kraev et al., 2001 [PubMed 11294880]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_020689.4

Inheritance

—

ClinVar variants

U:89B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr20:19,212,642-19,722,926

External References & Databases

Ensembl (ENSG00000185052)

Transcript & Mutation Effects

hg38 • Region Span ~510.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC24A3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020689.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	1 clinvar	4
missense			85 clinvar	1 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	89	2	1	92

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020689.4	RefSeq	NP_065740.2	17	MANE Select
ENST00000328041.11	Ensembl	ENSP00000333519.5	17	MANE Select
ENST00000962751.1	Ensembl	ENSP00000632810.1	15	Standard
ENST00000962751.2	Ensembl	ENSP00000632810.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sodium/Calcium exchangers
Transport of inorganic cations/anions and amino acids/oligopeptides
SLC-mediated transmembrane transport
Transport of small molecules

Biological Process

ion transport
potassium ion transport
cellular calcium ion homeostasis
sodium ion transmembrane transport
calcium ion transmembrane transport

Molecular Function

calcium channel activity
calcium, potassium:sodium antiporter activity
symporter activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328041
Coding exons: 17
Length: 510292
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.09	264	378	0.698	0.0000218	4219
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+). {ECO:0000250}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.308
RVIS EVS: 1.14
RVIS percentile EVS: 92.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.119

Gene Damage Prediction

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