SLC66A1

solute carrier family 66 member 1, the group of Solute carrier family 66

Basic information

Region (hg38): 1:19312326-19329300

Previous symbols: [ "PQLC2" ]

Links

ENSG00000040487 ∙ NCBI:54896 ∙ OMIM:614760 ∙ HGNC:26001 ∙ Uniprot:Q6ZP29 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC66A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC66A1 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						0
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in SLC66A1

This is a list of pathogenic ClinVar variants found in the SLC66A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-19317720-C-G		not specified	Uncertain significance (Jun 11, 2024)
1-19317726-G-A		not specified	Uncertain significance (Jan 06, 2023)
1-19324643-A-G		not specified	Uncertain significance (Apr 05, 2023)
1-19324656-C-T		not specified	Uncertain significance (Nov 25, 2024)
1-19324667-G-A		not specified	Uncertain significance (Dec 31, 2023)
1-19324683-T-C		not specified	Uncertain significance (Aug 15, 2024)
1-19324716-C-T		not specified	Uncertain significance (Sep 12, 2023)
1-19325526-A-C		not specified	Uncertain significance (Apr 26, 2023)
1-19325541-C-T		not specified	Uncertain significance (Sep 03, 2024)
1-19325571-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-19326265-G-T		not specified	Uncertain significance (Feb 06, 2024)
1-19326272-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-19326280-A-G		not specified	Uncertain significance (Jun 09, 2022)
1-19326290-C-T		not specified	Likely benign (Oct 27, 2021)
1-19326304-C-A		not specified	Uncertain significance (Dec 04, 2024)
1-19326332-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-19326355-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-19326359-C-T		not specified	Uncertain significance (Jun 10, 2024)
1-19326580-G-A		not specified	Uncertain significance (Nov 06, 2024)
1-19326591-C-G		not specified	Uncertain significance (Aug 19, 2023)
1-19326616-G-A		not specified	Uncertain significance (Aug 28, 2024)
1-19326621-AACGTGAGCCTCC-A		Nephropathic cystinosis	Uncertain significance (Mar 25, 2024)
1-19327249-G-T		not specified	Uncertain significance (Oct 08, 2024)
1-19327269-G-A		not specified	Uncertain significance (Apr 29, 2024)
1-19327270-C-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC66A1	protein_coding	protein_coding	ENST00000375153	7	16975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000635	0.909	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.976	149	187	0.799	0.0000122	1848
Missense in Polyphen		29	50.553	0.57365		523
Synonymous	0.669	83	91.1	0.911	0.00000646	632
Loss of Function	1.56	9	15.6	0.575	9.61e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000131	0.0000924
European (Non-Finnish)	0.000234	0.000229
Middle Eastern	0.000164	0.000163
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Amino acid transporter that specifically mediates the pH-dependent export of the cationic amino acids arginine, histidine and lysine from lysosomes. {ECO:0000269|PubMed:22822152, ECO:0000269|PubMed:23169667}.
• Pathway: Transport of small molecules;Miscellaneous transport and binding events (Consensus)

Intolerance Scores

• loftool: 0.295
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.301
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.434

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pqlc2

Gene ontology

• Biological process: arginine transport;lysine transport;transmembrane transport;amino acid homeostasis;L-lysine transmembrane transport;arginine transmembrane transport
• Cellular component: lysosomal membrane;integral component of organelle membrane;intracellular membrane-bounded organelle
• Molecular function: basic amino acid transmembrane transporter activity;arginine transmembrane transporter activity;L-lysine transmembrane transporter activity