SLC12A4

solute carrier family 12 member 4, the group of Solute carrier family 12

Basic information

Region (hg38): 16:67943474-67969601

Links

ENSG00000124067

∙ NCBI:6560 ∙ OMIM:604119 ∙ HGNC:10913 ∙ Uniprot:Q9UP95 ∙ 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 SLC12A4 gene.

not_specified (149 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC12A4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005072.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			139 clinvar	7 clinvar		146
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	142	8	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC12A4	protein_coding	protein_coding	ENST00000422611	23	26128

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.05e-11	1.00	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	594	694	0.855	0.0000447	7000
Missense in Polyphen		272	331.63	0.82019		3369
Synonymous	-0.989	318	296	1.07	0.0000202	2280
Loss of Function	3.48	27	54.8	0.493	0.00000282	566

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000824	0.000812
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000943	0.0000924
European (Non-Finnish)	0.000294	0.000290
Middle Eastern	0.000218	0.000217
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. May be involved in the regulation of basolateral Cl(-) exit in NaCl absorbing epithelia (By similarity). Isoform 4 has no transport activity. {ECO:0000250}.;
Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Cation-coupled Chloride cotransporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

pRec: 0.272

Intolerance Scores

loftool: 0.0282
rvis_EVS: -1.92
rvis_percentile_EVS: 1.93

Haploinsufficiency Scores

pHI: 0.429
hipred: Y
hipred_score: 0.597
ghis: 0.669

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc12a4
Phenotype: immune system phenotype; renal/urinary system phenotype; respiratory system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: ion transport;cell volume homeostasis;chemical synaptic transmission;chloride ion homeostasis;potassium ion homeostasis;chloride transmembrane transport;potassium ion import across plasma membrane
Cellular component: lysosomal membrane;plasma membrane;integral component of plasma membrane;membrane
Molecular function: potassium:chloride symporter activity;protein kinase binding