MFSD2B

protein-coding

MFSD2 lysolipid transporter B, sphingolipid, the group of Solute carrier family 59

Gene summary

Predicted to enable symporter activity. Involved in lipid transport. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001346880.2

Inheritance

—

ClinVar variants

U:58B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr2:24,010,081-24,063,321

External References & Databases

Ensembl (ENSG00000205639)

Transcript & Mutation Effects

hg38 • Region Span ~53.2 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 MFSD2B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001346880.2. 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			58 clinvar	3 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	4	0	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001346880.2	RefSeq	NP_001333809.1	14	MANE Select
ENST00000338315.6	Ensembl	ENSP00000342501.4	14	MANE Select
ENST00000406420.7	Ensembl	ENSP00000385527.3	13	Standard
ENST00000406420.8	Ensembl	ENSP00000385527.3	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid transport
carbohydrate transport
transmembrane transport
organic substance transport

Molecular Function

transporter activity
symporter activity
sphingolipid transporter activity

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000406420
Coding exons: 13
Length: 53241
Individuals with no LoFs: 124698
Homozygous LoFs: 0
Heterozygous LoFs: 83
Defined: 124781
p: 0.000333

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.226	274	285	0.962	0.0000166	3099
Missense (PolyPhen)		111	112.96	0.98263		1244
Synonymous	-0.224	137	134	1.02	0.00000890	1113
Loss of Function	0.798	18	22.0	0.817	0.00000103	255

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00040	0.00038	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0017	0.0017	notable
Finnish	0.00042	0.00037	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000099	0.000098	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cation-dependent lipid transporter that specifically mediates export of sphingosine-1-phosphate in red blood cells and platelets (PubMed:29045386). Sphingosine-1-phosphate is a signaling sphingolipid and its export from red blood cells into in the plasma is required for red blood cell morphology (By similarity). Does not transport lysophosphatidylcholine (LPC) (By similarity). {ECO:0000250|UniProtKB:Q3T9M1, ECO:0000269|PubMed:29045386}.;

Intolerance Scores

LoFtool: 0.464
RVIS EVS: 0.44
RVIS percentile EVS: 77.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.283

Gene Damage Prediction

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