SLC16A13
Basic information
Region (hg38): 17:7036015-7040117
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (49 variants)
- Short_stature_with_nonspecific_skeletal_abnormalities_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC16A13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000201566.3. 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 | 0 | |||||
| missense | 46 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 46 | 3 | 0 |
Highest pathogenic variant AF is 6.853136e-7
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC16A13 | protein_coding | protein_coding | ENST00000308027 | 4 | 4047 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.57e-11 | 0.0254 | 125683 | 0 | 65 | 125748 | 0.000258 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.181 | 228 | 236 | 0.967 | 0.0000127 | 2650 |
| Missense in Polyphen | 85 | 92.973 | 0.91424 | 1055 | ||
| Synonymous | 0.860 | 98 | 109 | 0.895 | 0.00000576 | 1040 |
| Loss of Function | -0.463 | 15 | 13.2 | 1.14 | 7.54e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000576 | 0.000575 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00109 | 0.00109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000203 | 0.000202 |
| Middle Eastern | 0.00109 | 0.00109 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Proton-linked monocarboxylate transporter. May catalyze the transport of monocarboxylates across the plasma membrane. {ECO:0000305|PubMed:12739169}.;
- Disease
- DISEASE: Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:24390345}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Glycosphingolipid metabolism;Glycerophospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.889
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.92
Haploinsufficiency Scores
- pHI
- 0.0300
- hipred
- N
- hipred_score
- 0.282
- ghis
- 0.486
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.316
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc16a13
- Phenotype
Gene ontology
- Biological process
- monocarboxylic acid transport;transmembrane transport
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of plasma membrane
- Molecular function
- monocarboxylic acid transmembrane transporter activity;symporter activity