SPNS3

protein-coding

SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative), the group of Solute carrier family 63, sphingosine phosphate transporters

Gene summary

Predicted to enable transmembrane transporter activity. Predicted to be involved in lipid transport and transmembrane transport. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_182538.5

Inheritance

—

ClinVar variants

U:104B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr17:4,433,940-4,488,208

External References & Databases

Ensembl (ENSG00000182557)

Transcript & Mutation Effects

hg38 • Region Span ~54.3 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 SPNS3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182538.5. 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			2 clinvar	1 clinvar		3
missense			102 clinvar	11 clinvar		113
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	12	0	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182538.5	RefSeq	NP_872344.3	12	MANE Select
ENST00000355530.7	Ensembl	ENSP00000347721.2	12	MANE Select
NM_001320449.2	RefSeq	NP_001307378.1	10	Standard
ENST00000575194.5	Ensembl	ENSP00000460781.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid transport
transmembrane transport

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355530
Coding exons: 12
Length: 54521
Individuals with no LoFs: 125012
Homozygous LoFs: 2
Heterozygous LoFs: 734
Defined: 125748
p: 0.00293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.338	301	318	0.947	0.0000203	3207
Missense (PolyPhen)		84	90.63	0.92685		931
Synonymous	-2.29	178	143	1.24	0.0000100	1120
Loss of Function	0.621	20	23.2	0.861	0.00000108	250

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0017	0.0017	notable
Latino/Admixed American	0.00088	0.00087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.0028	0.0025	notable
European (Non-Finnish)	0.0050	0.0050	notable
South Asian	0.0016	0.0014	notable
Other	0.0015	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sphingolipid transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.0875

Intolerance Scores

LoFtool: 0.789
RVIS EVS: -0.15
RVIS percentile EVS: 42.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

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