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

ClinVar

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

• not_specified (114 variants)
• not_provided (1 variants)
• See_cases (1 variants)

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. These statistics are base on transcript: NM_000020246.4. 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				1	1	2
missense			111	3		114
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	111	4	1

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