SLC7A14

protein-coding

solute 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

NM_020949.3

Inheritance

AD, AR

ClinVar variants

P:4U:398B:184

Top phenotype

Retinitis pigmentosa 68

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr3:170,459,548-170,586,075

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~126.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

retinitis pigmentosa 68NO_KNOWN

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).

retinitis pigmentosa 68LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014323

Submitter: PanelApp Australia

retinitis pigmentosa 68LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0014323

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosa 68STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014323

Submitter: G2P

Clinical Genomic Database (CGD)

Retinitis pigmentosa 68AR

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

Refs: 24670872Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC7A14 variants in ClinVar

7 Conditions Cataloged
not providedTotal: 596
not specifiedTotal: 210
Retinal dystrophyTotal: 42
Retinitis pigmentosa 68Total: 11
SLC7A14-related disorderTotal: 10
Optic atrophyTotal: 1
Retinitis pigmentosaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
160
clinvar
4
clinvar
168
missense
2
clinvar
2
clinvar
376
clinvar
18
clinvar
2
clinvar
400
nonsense
9
clinvar
9
start loss
0
frameshift
7
clinvar
7
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total223981786586
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020949.3RefSeqNP_066000.27MANE Select
ENST00000231706.6EnsemblENSP00000231706.47MANE Select
ENST00001107543.1EnsemblENSP00000777348.16Standard
ENST00001143803.1EnsemblENSP00000802044.17Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
slc7a14aDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.7834054520.8960.00002565001
Missense (PolyPhen)145170.130.852281850
Synonymous-0.01841931931.000.00001261607
Loss of Function3.35826.70.3000.00000134317

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000380.00038rare
Finnish00.0absent
European (Non-Finnish)0.0000710.000070rare
South Asian00.0absent
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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