SLC66A2

protein-coding

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

Gene summary

Predicted to be involved in phospholipid translocation and retrograde transport, endosome to Golgi. Predicted to be located in cytosol and membrane. Predicted to be active in endosome membrane and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PQLC1

MANE transcript

NM_025078.5

Inheritance

—

ClinVar variants

U:54B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr18:79,902,420-79,951,657

External References & Databases

Ensembl (ENSG00000122490)

Transcript & Mutation Effects

hg38 • Region Span ~49.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC66A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025078.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	1 clinvar	4
missense			50 clinvar	4 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	54	7	1	62

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 105 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025078.5	RefSeq	NP_079354.2	5	MANE Select
ENST00000397778.7	Ensembl	ENSP00000380880.2	5	MANE Select
NM_001146343.2	RefSeq	NP_001139815.1	3	Standard
NM_001146345.2	RefSeq	NP_001139817.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

retrograde transport, endosome to Golgi
phospholipid translocation

Cellular Component

endosome
trans-Golgi network
cytosol
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397778
Coding exons: 5
Length: 49245
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125745
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0997	181	177	1.02	0.0000111	1742
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000065	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.107
RVIS EVS: -0.31
RVIS percentile EVS: 31.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.160

Gene Damage Prediction

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