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.

• not_specified (48 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000025078.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			41	4		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	7	1

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