SLC7A14

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

Basic information

Region (hg38): 3:170459547-170586075

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 (433 variants)
• Inborn genetic diseases (39 variants)
• Retinitis pigmentosa 68 (8 variants)
• not specified (5 variants)
• Retinal dystrophy (2 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				116	8	124
missense			244	8	5	257
nonsense			6			6
start loss						0
frameshift			6			6
inframe indel			4			4
splice donor/acceptor (+/-2bp)			1			1
splice region			5	7	1	13
non coding			1	25	3	29
Total	0	0	262	149	16

Variants in SLC7A14

This is a list of pathogenic ClinVar variants found in the SLC7A14 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-170467055-C-G			Uncertain significance (Aug 04, 2020)
3-170467065-G-C			Uncertain significance (Sep 08, 2023)
3-170467074-A-G		not specified	Uncertain significance (Dec 22, 2023)
3-170467079-A-T			Uncertain significance (Feb 05, 2022)
3-170467081-C-A			Uncertain significance (Oct 01, 2020)
3-170467089-A-G		Retinal dystrophy • not specified	Uncertain significance (Oct 03, 2023)
3-170467091-C-T			Likely benign (Aug 28, 2023)
3-170467094-G-A			Benign (Dec 11, 2023)
3-170467110-T-C			Uncertain significance (Oct 17, 2022)
3-170467114-GTTTGCT-G			Uncertain significance (Jul 07, 2023)
3-170467116-T-G			Uncertain significance (Dec 03, 2023)
3-170467130-C-T		SLC7A14-related disorder	Likely benign (Jun 05, 2023)
3-170467139-A-C			Uncertain significance (Oct 26, 2022)
3-170467139-A-G			Likely benign (Feb 16, 2023)
3-170467145-C-T		not specified	Benign/Likely benign (Jan 31, 2024)
3-170467146-C-T		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
3-170467147-G-A			Uncertain significance (Apr 24, 2023)
3-170467148-G-A			Likely benign (Jul 06, 2022)
3-170467150-C-T			Uncertain significance (Dec 01, 2023)
3-170467154-T-C			Likely benign (May 12, 2023)
3-170467157-C-T			Likely benign (Nov 30, 2022)
3-170467160-C-T			Likely benign (Jan 25, 2024)
3-170467161-G-A			Benign (Jan 31, 2024)
3-170467175-T-C			Likely benign (Aug 16, 2022)
3-170467183-A-G		not specified	Uncertain significance (Jan 23, 2023)

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