SLC12A9
Basic information
Region (hg38): 7:100826820-100867010
Links
Phenotypes
GenCC
Source:
- 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
- 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 111 | 114 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 111 | 4 | 1 |
GnomAD
Source:
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:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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