SLC4A3

solute carrier family 4 member 3, the group of Solute carrier family 4

Basic information

Region (hg38): 2:219627394-219641980

Links

ENSG00000114923 ∙ NCBI:6508 ∙ OMIM:106195 ∙ HGNC:11029 ∙ Uniprot:P48751 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short QT syndrome 7 (Moderate), mode of inheritance: AD
• short QT syndrome (Moderate), mode of inheritance: AD
• short QT syndrome 7 (Strong), mode of inheritance: AD
• short QT syndrome 7 (Strong), mode of inheritance: AD
• short QT syndrome (Moderate), mode of inheritance: AD
• autosomal dominant distal renal tubular acidosis (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short QT syndrome 7	AD	Cardiovascular	The condition includes increased risk of arrhythmia, cardiomyopathy, and adverse cardiac outcomes, and identification may enable interventions	Cardiovascular	29167417

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC4A3 gene.

• Inborn_genetic_diseases (190 variants)
• not_provided (44 variants)
• not_specified (38 variants)
• SLC4A3-related_disorder (12 variants)
• Short_QT_syndrome_7 (6 variants)
• Cardiovascular_phenotype (3 variants)
• Incidental_Discovery (1 variants)
• Cardiomyopathy (1 variants)
• Cardiac_arrhythmia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC4A3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005070.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	23	8	36
missense	1	1	207	11		220
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	1	1	215	34	8

Highest pathogenic variant AF is 0.0000049563223

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC4A3	protein_coding	protein_coding	ENST00000373762	22	14654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125702	0	44	125746	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	571	787	0.725	0.0000513	8031
Missense in Polyphen		206	354.34	0.58135		3574
Synonymous	0.690	327	343	0.953	0.0000226	2730
Loss of Function	4.25	18	50.7	0.355	0.00000285	548

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000393	0.000388
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.000116	0.000109
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000153	0.000149
Middle Eastern	0.000116	0.000109
South Asian	0.000197	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plasma membrane anion exchange protein of wide distribution. Mediates at least a part of the Cl(-)/HCO3(-) exchange in cardiac myocytes. Both BAE3 and CAE3 forms transport Cl(-).
• Pathway: Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters (Consensus)

Recessive Scores

• pRec: 0.296

Intolerance Scores

• rvis_EVS: -1.18
• rvis_percentile_EVS: 5.92

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.842

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: slc4a3
• Affected structure: heart
• Phenotype tag: abnormal
• Phenotype quality: functionality

Gene ontology

• Biological process: inorganic anion transport;bicarbonate transport;regulation of intracellular pH;anion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: inorganic anion exchanger activity;anion:anion antiporter activity