SLC12A9

solute carrier family 12 member 9, the group of Solute carrier family 12

Basic information

Region (hg38): 7:100826820-100867010

Links

ENSG00000146828 ∙ NCBI:56996 ∙ OMIM:616861 ∙ HGNC:17435 ∙ Uniprot:Q9BXP2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC12A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC12A9 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			49	2		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	2	1

Variants in SLC12A9

This is a list of pathogenic ClinVar variants found in the SLC12A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100826955-G-GC			Benign (May 14, 2021)
7-100826959-C-CA			Likely benign (Feb 08, 2023)
7-100826962-CCCG-C			Likely benign (Sep 04, 2023)
7-100826963-CCG-C			Benign (Feb 01, 2024)
7-100826963-C-CG			Benign (Jan 08, 2024)
7-100826964-CG-GC			Uncertain significance (Dec 07, 2022)
7-100826964-CG-C			Benign (Jan 31, 2024)
7-100826965-G-C		Capillary malformation-arteriovenous malformation 2 • Lymphatic malformation 7	Benign (Jan 31, 2024)
7-100826965-G-T			Likely benign (Nov 13, 2023)
7-100826965-G-GC			Benign (Aug 28, 2023)
7-100826989-T-C		Cardiovascular phenotype	Likely benign (Mar 26, 2023)
7-100826990-G-A		Cardiovascular phenotype	Uncertain significance (Apr 22, 2023)
7-100826991-C-T		Cardiovascular phenotype	Conflicting classifications of pathogenicity (Sep 09, 2023)
7-100826997-A-G		Cardiovascular phenotype	Likely benign (Feb 14, 2020)
7-100826997-AC-A		Capillary malformation-arteriovenous malformation 2	Pathogenic (Nov 21, 2018)
7-100827000-A-T		Cardiovascular phenotype	Uncertain significance (Jul 27, 2020)
7-100827002-G-T			Uncertain significance (Dec 29, 2020)
7-100827003-C-A			Uncertain significance (Mar 10, 2022)
7-100827003-C-G			Uncertain significance (Mar 16, 2022)
7-100827003-C-T		Cardiovascular phenotype	Uncertain significance (Oct 21, 2022)
7-100827013-C-G		Cardiovascular phenotype	Likely benign (Mar 07, 2021)
7-100827014-A-T			Uncertain significance (Aug 01, 2023)
7-100827016-C-T		Cardiovascular phenotype	Likely benign (Dec 10, 2023)
7-100827018-C-A		Cardiovascular phenotype	Uncertain significance (Apr 12, 2023)
7-100827018-C-T		Cardiovascular phenotype	Likely benign (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC12A9	protein_coding	protein_coding	ENST00000354161	13	40190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-15	0.0773	125596	0	152	125748	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	413	578	0.714	0.0000376	5709
Missense in Polyphen		117	198.19	0.59034		2016
Synonymous	-0.346	279	272	1.03	0.0000178	2194
Loss of Function	0.852	26	31.1	0.835	0.00000159	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000717	0.000655
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00337	0.00180
European (Non-Finnish)	0.000728	0.000695
Middle Eastern	0.0000544	0.0000544
South Asian	0.000364	0.000359
Other	0.000816	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be an inhibitor of SLC12A1. Seems to correspond to a subunit of a multimeric transport system and thus, additional subunits may be required for its function. {ECO:0000269|PubMed:10871601}.

Recessive Scores

• pRec: 0.158

Intolerance Scores

• rvis_EVS: -1.17
• rvis_percentile_EVS: 6.06

Haploinsufficiency Scores

• pHI: 0.232
• hipred: N
• hipred_score: 0.463
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.772

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc12a9

Gene ontology

• Biological process: cell volume homeostasis;chloride ion homeostasis;potassium ion homeostasis;chloride transmembrane transport;potassium ion import across plasma membrane
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: cation:chloride symporter activity;potassium:chloride symporter activity