SLC66A2

solute carrier family 66 member 2, the group of Solute carrier family 66

Basic information

Region (hg38): 18:79902420-79951657

Previous symbols: [ "PQLC1" ]

Links

ENSG00000122490 ∙ NCBI:80148 ∙ ∙ HGNC:26188 ∙ Uniprot:Q8N2U9 ∙ 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 SLC66A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC66A2 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				2	1	3
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	1

Variants in SLC66A2

This is a list of pathogenic ClinVar variants found in the SLC66A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-79904005-C-T		not specified	Uncertain significance (Mar 07, 2024)
18-79904008-C-T		not specified	Uncertain significance (Sep 11, 2024)
18-79904019-G-A		not specified	Uncertain significance (May 17, 2023)
18-79904080-C-A		not specified	Uncertain significance (Jun 07, 2022)
18-79904098-C-T		not specified	Uncertain significance (Nov 18, 2022)
18-79904135-G-C		not specified	Likely benign (Dec 04, 2024)
18-79904146-A-C		not specified	Uncertain significance (Jul 17, 2024)
18-79904150-G-A		not specified	Likely benign (May 14, 2024)
18-79919192-C-A		not specified	Uncertain significance (Jan 24, 2024)
18-79919209-G-A		not specified	Uncertain significance (Oct 16, 2024)
18-79919218-G-A		not specified	Uncertain significance (Dec 05, 2022)
18-79919221-A-G		not specified	Uncertain significance (Mar 12, 2024)
18-79919242-T-C		not specified	Uncertain significance (May 26, 2023)
18-79919249-G-A			Benign (May 16, 2018)
18-79919299-T-C		not specified	Uncertain significance (Jun 30, 2023)
18-79919326-C-T		not specified	Uncertain significance (Dec 13, 2023)
18-79919372-C-G		not specified	Uncertain significance (Jun 19, 2024)
18-79919376-T-C		not specified	Uncertain significance (Apr 27, 2022)
18-79919383-A-C		not specified	Uncertain significance (Mar 27, 2023)
18-79919395-C-T		not specified	Uncertain significance (Dec 21, 2023)
18-79933981-G-A		not specified	Uncertain significance (Feb 28, 2023)
18-79943344-G-A		not specified	Uncertain significance (Oct 06, 2021)
18-79943452-G-A		not specified	Uncertain significance (Dec 27, 2022)
18-79950736-C-T		not specified	Uncertain significance (Nov 13, 2024)
18-79950786-G-T		not specified	Likely benign (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC66A2	protein_coding	protein_coding	ENST00000397778	5	49245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0103	0.949	125723	0	22	125745	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0997	181	177	1.02	0.0000111	1742
Missense in Polyphen		26	44.798	0.58038		512
Synonymous	-2.44	112	83.6	1.34	0.00000579	585
Loss of Function	1.78	5	11.5	0.434	4.96e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000118	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.107
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.261
• hipred: N
• hipred_score: 0.350
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pqlc1

Gene ontology

• Biological process: retrograde transport, endosome to Golgi;phospholipid translocation
• Cellular component: endosome;trans-Golgi network;cytosol;integral component of membrane