SLC66A3

solute carrier family 66 member 3, the group of Solute carrier family 66

Basic information

Region (hg38): 2:11155198-11178870

Previous symbols: [ "C2orf22", "PQLC3" ]

Links

ENSG00000162976 ∙ NCBI:130814 ∙ ∙ HGNC:28503 ∙ Uniprot:Q8N755 ∙ 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 SLC66A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC66A3 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in SLC66A3

This is a list of pathogenic ClinVar variants found in the SLC66A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-11155572-G-A		not specified	Uncertain significance (Feb 13, 2024)
2-11155576-C-A		not specified	Uncertain significance (Oct 05, 2023)
2-11155614-C-G		not specified	Uncertain significance (Nov 08, 2022)
2-11155632-T-C		not specified	Uncertain significance (Mar 23, 2023)
2-11155672-A-C		not specified	Uncertain significance (Jul 26, 2022)
2-11155679-G-C		not specified	Uncertain significance (Dec 06, 2021)
2-11160482-C-T		not specified	Uncertain significance (Jun 17, 2024)
2-11160483-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-11160666-G-A		not specified	Uncertain significance (Aug 13, 2021)
2-11164206-T-G		not specified	Uncertain significance (Mar 30, 2024)
2-11164244-A-G		not specified	Uncertain significance (Feb 03, 2022)
2-11171946-G-A		not specified	Uncertain significance (Aug 21, 2023)
2-11171986-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-11171994-T-G		not specified	Uncertain significance (Oct 06, 2021)
2-11172034-A-G		not specified	Uncertain significance (Aug 04, 2023)
2-11174974-T-A		not specified	Uncertain significance (Dec 16, 2023)
2-11174992-C-A		not specified	Uncertain significance (Jun 16, 2024)
2-11174998-A-G		not specified	Uncertain significance (Apr 06, 2023)
2-11177796-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC66A3	protein_coding	protein_coding	ENST00000295083	7	23677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.43e-10	0.0302	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.521	94	109	0.860	0.00000644	1260
Missense in Polyphen		30	28.166	1.0651		373
Synonymous	1.02	39	48.0	0.812	0.00000317	414
Loss of Function	-0.669	13	10.6	1.22	4.53e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00245	0.00243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00141
Finnish	0.00	0.00
European (Non-Finnish)	0.000129	0.000123
Middle Eastern	0.00141	0.00141
South Asian	0.000275	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.618
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.248
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.112

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pqlc3

Gene ontology

• Cellular component: integral component of membrane