SLC7A10
protein-codingsolute carrier family 7 member 10, the group of Solute carrier family 7
Gene summary
SLC7A10, in association with 4F2HC (SLC3A2; MIM 158070), mediates high-affinity transport of D-serine and several other neutral amino acids (Nakauchi et al., 2000 [PubMed 10863037]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.2 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 SLC7A10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_019849.3. 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 | 1 | 2 | 3 | |||
| missense | 84 | 11 | 1 | 96 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 86 | 11 | 3 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_062823.1 | 11 | MANE Select | |
| Ensembl | ENSP00000253188.2 | 11 | MANE Select | |
| Ensembl | ENSP00000466876.1 | 2 | Standard | |
| Ensembl | ENSP00000465421.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Differentiation of white and brown adipocyte
- Amino acid transport across the plasma membrane
- Amino acid and oligopeptide SLC transporters
- Transport of inorganic cations/anions and amino acids/oligopeptides
- SLC-mediated transmembrane transport
Biological Process
- amino acid transmembrane transport
- amino acid transport
- neutral amino acid transport
- L-serine transport
- D-alanine transport
Molecular Function
- neutral amino acid transmembrane transporter activity
- L-amino acid transmembrane transporter activity
- L-serine transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000253188
- Coding exons
- 11
- Length
- 17187
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 42
- Defined
- 125743
- p
- 0.000167
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.11 | 265 | 321 | 0.826 | 0.0000199 | 3312 |
| Missense (PolyPhen) | 113 | 135.23 | 0.83562 | 1429 | ||
| Synonymous | 0.266 | 148 | 152 | 0.973 | 0.0000112 | 1124 |
| Loss of Function | 2.36 | 10 | 21.9 | 0.456 | 0.00000103 | 237 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00020 | 0.00018 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00014 | 0.00013 | rare |
| South Asian | 0.00067 | 0.00065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sodium-independent, high affinity transport of small neutral D- and L-amino acids. May play a role in the modulation of glutamatergic transmission through mobilization of D-serine at the glutamatergic synapse. {ECO:0000269|PubMed:10863037}.;
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- LoFtool
- 0.181
- RVIS EVS
- -0.57
- RVIS percentile EVS
- 18.9
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.146
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |