SPNS1

protein-coding

SPNS lysolipid transporter 1, lysophospholipid, the group of Solute carrier family 63, sphingosine phosphate transporters

Gene summary

Enables lysophospholipid:sodium symporter activity. Involved in lysophospholipid transport. Located in lysosomal membrane. Is active in lysosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032038.3

Inheritance

—

ClinVar variants

U:64B:7

Top phenotype

Elevated circulating hepatic transaminase concentration

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr16:28,974,221-28,984,548

External References & Databases

Ensembl (ENSG00000169682)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 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 SPNS1 variants in ClinVar

11 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 4

Elevated circulating hepatic transaminase concentrationTotal: 2

Motor delayTotal: 2

HyperbilirubinemiaTotal: 2

FatigueTotal: 2

Attention deficit hyperactivity disorderTotal: 2

MyalgiaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032038.3. 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	3 clinvar	1 clinvar	5
missense			55 clinvar	3 clinvar		58
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	64	6	1	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032038.3	RefSeq	NP_114427.1	12	MANE Select
ENST00000311008.16	Ensembl	ENSP00000309945.11	12	MANE Select
NM_001142448.2	RefSeq	NP_001135920.1	12	Standard
NM_001142449.2	RefSeq	NP_001135921.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
spns1	Danio rerio	Structure: cell Quality: accumulation abnormal

Gene / Model

Organism

Observed Phenotype

spns1

Danio rerio

Structure: cell

Quality: accumulation

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid transport
transmembrane transport

Molecular Function

protein binding

Cellular Component

mitochondrial inner membrane
lysosomal membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311008
Coding exons: 12
Length: 10328
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125747
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.06	237	344	0.688	0.0000226	3318
Missense (PolyPhen)		62	125.75	0.49303		1269
Synonymous	0.797	137	149	0.917	0.00000962	1210
Loss of Function	2.97	7	22.1	0.317	0.00000103	229

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death. {ECO:0000250, ECO:0000269|PubMed:12815463}.;

Recessive Scores

pRec: 0.300

Intolerance Scores

LoFtool: 0.579
RVIS EVS: -0.58
RVIS percentile EVS: 18.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.971

Gene Damage Prediction

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