SLC7A14

solute carrier family 7 member 14, the group of Protein phosphatase 1 regulatory subunits|Solute carrier family 7

Basic information

Region (hg38): 3:170459548-170586075

Links

ENSG00000013293

∙ NCBI:57709 ∙ OMIM:615720 ∙ HGNC:29326 ∙ Uniprot:Q8TBB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Supportive), mode of inheritance: AD
retinitis pigmentosa 68 (Strong), mode of inheritance: AR
retinitis pigmentosa 68 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 68	AR	General	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	Ophthalmologic	24670872

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC7A14 gene.

not_provided (517 variants)
not_specified (121 variants)
Retinal_dystrophy (44 variants)
Retinitis_pigmentosa_68 (11 variants)
SLC7A14-related_disorder (9 variants)
Optic_atrophy (1 variants)
Retinitis_pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020949.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	142 clinvar	7 clinvar	154
missense	2 clinvar	2 clinvar	321 clinvar	12 clinvar	4 clinvar	341
nonsense			8 clinvar			8
start loss						0
frameshift			7 clinvar			7
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	2	2	343	154	11

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A14	protein_coding	protein_coding	ENST00000231706	7	126492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0221	0.978	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.783	405	452	0.896	0.0000256	5001
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000381	0.000381
South Asian	0.00	0.00
Other	0.000168	0.000163

dbNSFP

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

Haploinsufficiency Scores

pHI: 0.161
hipred: Y
hipred_score: 0.652
ghis: 0.551

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.343

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Slc7a14
Phenotype: vision/eye phenotype;

Zebrafish Information Network

Gene name: slc7a14a
Affected structure: trunk
Phenotype tag: abnormal
Phenotype quality: malformed

Gene ontology

Biological process: amino acid transport;negative regulation of phosphatase activity;transmembrane transport
Cellular component: lysosomal membrane;integral component of membrane
Molecular function: transmembrane transporter activity