SLC12A7

solute carrier family 12 member 7, the group of Solute carrier family 12|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:1050384-1112063

Links

ENSG00000113504 ∙ NCBI:10723 ∙ OMIM:604879 ∙ HGNC:10915 ∙ Uniprot:Q9Y666 ∙ 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 SLC12A7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC12A7 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				4	9	13
missense			97	10	3	110
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	3	4
non coding					58	58
Total	0	0	97	14	70

Variants in SLC12A7

This is a list of pathogenic ClinVar variants found in the SLC12A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-1052245-C-T			Benign (Nov 12, 2018)
5-1052373-G-A		not specified	Uncertain significance (May 11, 2022)
5-1052421-C-T		not specified	Uncertain significance (May 30, 2024)
5-1052620-GGAGCA-G			Benign (Jun 19, 2021)
5-1053101-G-C			Benign (Jun 19, 2021)
5-1053226-A-G			Benign (Nov 12, 2018)
5-1053281-C-G			Benign (Nov 12, 2018)
5-1053423-T-C		not specified	Likely benign (Aug 21, 2023)
5-1053469-C-T		not specified	Uncertain significance (May 22, 2023)
5-1053470-G-T		not specified	Uncertain significance (May 23, 2023)
5-1053637-A-G			Benign (Nov 12, 2018)
5-1057290-G-A			Benign (Nov 12, 2018)
5-1057500-A-G			Benign (Nov 12, 2018)
5-1057510-G-A		not specified	Uncertain significance (Dec 08, 2023)
5-1057523-T-C		not specified	Uncertain significance (Jun 24, 2022)
5-1057609-G-A		not specified	Uncertain significance (Aug 04, 2023)
5-1057610-C-A		not specified	Uncertain significance (Oct 22, 2024)
5-1057637-G-A		not specified	Uncertain significance (Jun 18, 2024)
5-1057667-T-C			Benign (Jun 19, 2021)
5-1057775-G-A			Benign (Jun 19, 2021)
5-1057845-C-T			Benign (Jun 19, 2021)
5-1060251-C-G			Benign (Nov 12, 2018)
5-1060264-G-A			Benign (Nov 12, 2018)
5-1060285-G-A			Benign (Jun 19, 2021)
5-1060348-C-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC12A7	protein_coding	protein_coding	ENST00000264930	24	61652

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.39e-17	0.884	125647	0	90	125737	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	622	722	0.861	0.0000511	6998
Missense in Polyphen		204	273.74	0.74523		2514
Synonymous	-3.05	419	347	1.21	0.0000295	2221
Loss of Function	2.23	35	52.4	0.668	0.00000263	554

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000469	0.000458
Ashkenazi Jewish	0.00	0.00
East Asian	0.000225	0.000217
Finnish	0.000673	0.000647
European (Non-Finnish)	0.000375	0.000360
Middle Eastern	0.000225	0.000217
South Asian	0.000630	0.000588
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May mediate K(+) uptake into Deiters' cells in the cochlea and contribute to K(+) recycling in the inner ear. Important for the survival of cochlear outer and inner hair cells and the maintenance of the organ of Corti. May be required for basolateral Cl(-) extrusion in the kidney and contribute to renal acidification (By similarity). {ECO:0000250, ECO:0000269|PubMed:10913127}.
• Pathway: Collecting duct acid secretion - Homo sapiens (human);Cation-coupled Chloride cotransporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.0914
• rvis_EVS: -2.79
• rvis_percentile_EVS: 0.65

Haploinsufficiency Scores

• pHI: 0.0975
• hipred: Y
• hipred_score: 0.693
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.224

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc12a7
• 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); hearing/vestibular/ear phenotype; renal/urinary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

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: plasma membrane;integral component of plasma membrane;protein-containing complex
• Molecular function: potassium:chloride symporter activity;protein kinase binding