SLC12A9

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

Basic information

Region (hg38): 7:100826820-100867010

Links

ENSG00000146828NCBI:56996OMIM:616861HGNC:17435Uniprot:Q9BXP2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
111
clinvar
3
clinvar
114
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 111 4 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC12A9protein_codingprotein_codingENST00000354161 1340190
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.18e-150.077312559601521257480.000605
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.444135780.7140.00003765709
Missense in Polyphen117198.190.590342016
Synonymous-0.3462792721.030.00001782194
Loss of Function0.8522631.10.8350.00000159330

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007170.000655
Ashkenazi Jewish0.00009920.0000992
East Asian0.00005440.0000544
Finnish0.003370.00180
European (Non-Finnish)0.0007280.000695
Middle Eastern0.00005440.0000544
South Asian0.0003640.000359
Other0.0008160.000489

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc12a9
Phenotype

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