SLC7A14
protein-codingsolute carrier family 7 member 14, the group of Protein phosphatase 1 regulatory subunits|Solute carrier family 7
Gene summary
This gene is predicted to encode a glycosylated, cationic amino acid transporter protein with 14 transmembrane domains. This gene is primarily expressed in skin fibroblasts, neural tissue, and primary endothelial cells and its protein is predicted to mediate lysosomal uptake of cationic amino acids. Mutations in this gene are associated with autosomal recessive retinitis pigmentosa. In mice, this gene is expressed in the photoreceptor layer of the retina where its expression increases over the course of retinal development and persists in the mature retina. [provided by RefSeq, Apr 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~126.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019200
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014323
Submitter: ClinGen
*SLC7A14* was first reported in relation to autosomal recessive “retinitis pigmentosa 68” in 2014 (Jin et al, 2014, PMID: 24670872). Seven individuals have been reported with bi-allelic variants in this gene. All of these individuals are Chinese with onset of symptoms in childhood, and all are either homozygous for c.988G>A (p.Gly330Arg) or c.1391G>T (p.Cys464Phe), or compound heterozygous for one of those variants and another missense variant (Jin et al, 2014, PMID: 24670872; Guo et al, 2019, PMID: 30924391). Evidence suggests that the p.Gly330Arg variant affects protein localization (Jin et al, 2014, PMID: 24670872; Giffen et al, 2022, PMID: 35394837). In gnomAD v4.1.0, c.988G>A (p.Gly330Arg) and c.1391G>T (p.Cys464Phe) have minor allele frequencies (MAFs) in the East Asian population of 0.02079 (933/44,880 alleles, 11 homozygotes) and 0.01146 (514/44,856 alleles, 3 homozygotes), respectively. The ClinGen Retina Gene Curation Expert Panel considers these MAFs to be too high for these variants to be disease-causing. Additional studies have been conducted in Chinese and Japanese cohorts with retinopathy and no individuals with rare biallelic variants in SLC7A14 were identified (Sugahara et al, 2017, PMID: 27028480; Dan et al, 2020, PMID: 31960602). Individuals with heterozygous missense variants in these genes have been reported, but the clinical significance is unknown. Regarding experimental evidence, in mice, *SLC7A14* is mainly expressed in the brain, spinal cord and retina (inner nuclear layer and photoreceptor layer) (Jin et al, 2014, PMID: 24670872). The gene has a similar expression pattern in zebrafish. Knock-out mice, and knock in mice with the p.Gly330Arg variant exhibit abnormal ERGs and thinning of the retina, in addition to progressive hearing loss, recapitulating the disease phenotype in humans (Jin et al, 2014, PMID: 24670872; Giffen et al, 2022, PMID: 35394837). Zebrafish in which Slc7a14 expression has been knocked down using a morpholino approach tended to have small eyes and had an abnormal response to light-dark transitions (Jin et al, 2014, PMID: 24670872, Zhuang et al, 2019, PMID: 31921845). In summary, based on the high minor allele frequencies for the c.988G>A (p.Gly330Arg) and c.1391G>T (p.Cys464Phe) variants, the evidence supporting the relationship between *SLC7A14* and autosomal recessive “retinitis pigmentosa 68” has been disputed by the ClinGen Retina GCEP. More evidence is needed to either support or entirely refute the role that *SLC7A14* plays in this disease. This classification was approved by the ClinGen Retina GCEP on July 8, 2026 (SOP v12).
Inheritance Pattern: AR
Disease ID:MONDO:0014323
Submitter: PanelApp Australia
Inheritance Pattern: Unknown
Disease ID:MONDO:0014323
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014323
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC7A14 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020949.3. 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 | 4 | 160 | 4 | 168 | ||
| missense | 2 | 2 | 376 | 18 | 2 | 400 |
| nonsense | 9 | 9 | ||||
| start loss | 0 | |||||
| frameshift | 7 | 7 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 2 | 2 | 398 | 178 | 6 | 586 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066000.2 | 7 | MANE Select | |
| Ensembl | ENSP00000231706.4 | 7 | MANE Select | |
| Ensembl | ENSP00000777348.1 | 6 | Standard | |
| Ensembl | ENSP00000802044.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| slc7a14a | Danio rerio | Structure: trunk Quality: malformed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- amino acid transport
- negative regulation of phosphatase activity
- transmembrane transport
Molecular Function
- transmembrane transporter activity
Cellular Component
- lysosomal membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000231706
- Coding exons
- 7
- Length
- 126492
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 125747
- p
- 0.0000875
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.783 | 405 | 452 | 0.896 | 0.0000256 | 5001 |
| Missense (PolyPhen) | 145 | 170.13 | 0.85228 | 1850 | ||
| Synonymous | -0.0184 | 193 | 193 | 1.00 | 0.0000126 | 1607 |
| Loss of Function | 3.35 | 8 | 26.7 | 0.300 | 0.00000134 | 317 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in arginine transport. {ECO:0000269|PubMed:22787143, ECO:0000269|PubMed:24670872}.;
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- LoFtool
- 0.0539
- RVIS EVS
- -1.08
- RVIS percentile EVS
- 7.24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.343
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |