SLC22A16
protein-codingsolute carrier family 22 member 16, the group of Solute carrier family 22
Gene summary
This gene encodes a member of the organic zwitterion transporter protein family which transports carnitine. The encoded protein has also been shown to transport anticancer drugs like bleomycin (PMID: 20037140) successful treatment has been correlated with the level of activity of this transporter in tumor cells. [provided by RefSeq, Dec 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~52.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC22A16 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033125.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 103 | 7 | 1 | 111 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 103 | 7 | 2 | 112 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_149116.2 | 8 | MANE Select | |
| Ensembl | ENSP00000357915.3 | 8 | MANE Select | |
| Ensembl | ENSP00000328583.4 | 9 | Standard | |
| Ensembl | ENSP00000328583.4 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Doxorubicin Pathway (Cancer Cell), Pharmacodynamics
- Doxorubicin Pathway, Pharmacokinetics
- Doxorubicin Metabolism Pathway
- Transport of bile salts and organic acids, metal ions and amine compounds
- SLC-mediated transmembrane transport
Biological Process
- multicellular organism development
- spermatogenesis
- single fertilization
- organic cation transport
- amine transport
Molecular Function
- amine transmembrane transporter activity
- organic cation transmembrane transporter activity
- carnitine transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368919
- Coding exons
- 8
- Length
- 51955
- Individuals with no LoFs
- 125571
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 177
- Defined
- 125748
- p
- 0.000704
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.636 | 347 | 315 | 1.10 | 0.0000166 | 3748 |
| Missense (PolyPhen) | 126 | 115.92 | 1.087 | 1397 | ||
| Synonymous | -0.750 | 137 | 126 | 1.08 | 0.00000732 | 1152 |
| Loss of Function | -1.94 | 34 | 23.8 | 1.43 | 0.00000120 | 277 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00068 | 0.00068 | rare |
| Latino/Admixed American | 0.00087 | 0.00087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0010 | 0.0010 | notable |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: High affinity carnitine transporter; the uptake is partially sodium-ion dependent. Thought to mediate the L-carnitine secretion mechanism from testis epididymal epithelium into the lumen which is involved in the maturation of spermatozoa. Also transports organic cations such as tetraethylammonium (TEA) and doxorubicin. The uptake of TEA is inhibited by various organic cations. The uptake of doxorubicin is sodium-independent. {ECO:0000269|PubMed:12089149, ECO:0000269|PubMed:15963465}.;
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- LoFtool
- 0.671
- RVIS EVS
- 0.47
- RVIS percentile EVS
- 78.83
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.225
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |