SLC45A3
protein-codingsolute carrier family 45 member 3, the group of Solute carrier family 45
Gene summary
Predicted to enable sucrose:proton symporter activity. Predicted to be involved in several processes, including positive regulation of fatty acid biosynthetic process; positive regulation of glucose metabolic process; and regulation of oligodendrocyte differentiation. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jun 2026]
- PCANAP6
- PCANAP2
- PCANAP8
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.7 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 SLC45A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033102.3. 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 | 0 | |||||
| missense | 72 | 4 | 76 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 72 | 4 | 0 | 76 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_149093.1 | 4 | MANE Select | |
| Ensembl | ENSP00000356113.3 | 4 | MANE Select | |
| Ensembl | ENSP00000561144.1 | 4 | Standard | |
| Ensembl | ENSP00000561144.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- MicroRNAs in cancer - Homo sapiens (human)
- Transcriptional misregulation in cancer - Homo sapiens (human)
- SLC-mediated transmembrane transport
- Transport of small molecules
- Cellular hexose transport
Biological Process
- hexose transmembrane transport
- positive regulation of glucose metabolic process
- sucrose transport
- positive regulation of fatty acid biosynthetic process
- regulation of oligodendrocyte differentiation
Molecular Function
- sucrose:proton symporter activity
- sugar transmembrane transporter activity
Cellular Component
- plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367145
- Coding exons
- 4
- Length
- 22609
- Individuals with no LoFs
- 125718
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 125748
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.58 | 268 | 351 | 0.763 | 0.0000224 | 3453 |
| Missense (PolyPhen) | 73 | 108.99 | 0.66979 | 1150 | ||
| Synonymous | 1.21 | 142 | 161 | 0.879 | 0.00000988 | 1315 |
| Loss of Function | 1.99 | 6 | 14.1 | 0.427 | 6.64e-7 | 156 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0.00020 | 0.000099 | rare |
| East Asian | 0.00050 | 0.00049 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00013 | 0.000088 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- LoFtool
- 0.298
- RVIS EVS
- -0.53
- RVIS percentile EVS
- 20.78
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.506
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |