SLC46A3

protein-coding

solute carrier family 46 member 3, the group of Solute carrier family 46

Gene summary

The protein encoded by this gene is a member of a transmembrane protein family that transports small molecules across membranes. The encoded protein has been found in lysosomal membranes, where it can transport catabolites from the lysosomes to the cytoplasm. This protein has been shown to be an effective transporter of the cytotoxic drug maytansine, which is used in antibody-based targeting of cancer cells. [provided by RefSeq, Dec 2016]

MANE transcript

NM_181785.4

Inheritance

—

ClinVar variants

U:67B:3

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr13:28,700,064-28,718,970

External References & Databases

Ensembl (ENSG00000139508)

Transcript & Mutation Effects

hg38 • Region Span ~18.9 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 SLC46A3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 68

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181785.4. 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				1 clinvar		1
missense			67 clinvar	2 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	3	0	70

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181785.4	RefSeq	NP_861450.1	5	MANE Select
ENST00000266943.11	Ensembl	ENSP00000266943.7	5	MANE Select
NM_001135919.2	RefSeq	NP_001129391.1	6	Standard
NM_001347960.2	RefSeq	NP_001334889.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
transmembrane transport

Molecular Function

molecular_function

Cellular Component

integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380814
Coding exons: 6
Length: 18907
Individuals with no LoFs: 125517
Homozygous LoFs: 1
Heterozygous LoFs: 230
Defined: 125748
p: 0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.485	224	245	0.913	0.0000123	3005
Missense (PolyPhen)		58	71.004	0.81686		883
Synonymous	1.18	76	90.3	0.842	0.00000490	934
Loss of Function	0.962	15	19.6	0.766	0.00000118	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00096	0.00095	rare
Ashkenazi Jewish	0.00070	0.00069	rare
East Asian	0.00055	0.00054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.0011	0.0011	notable
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.734
RVIS EVS: 0
RVIS percentile EVS: 53.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

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