MFSD2B

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

Basic information

Region (hg38): 2:24010080-24063321

Links

ENSG00000205639 ∙ NCBI:388931 ∙ OMIM:617845 ∙ HGNC:37207 ∙ Uniprot:A6NFX1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MFSD2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD2B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in MFSD2B

This is a list of pathogenic ClinVar variants found in the MFSD2B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-24010107-C-T		not specified	Uncertain significance (Oct 14, 2023)
2-24010117-A-G			Likely benign (Jan 01, 2023)
2-24010160-C-G		not specified	Uncertain significance (Dec 09, 2023)
2-24010167-C-A		not specified	Uncertain significance (Oct 13, 2023)
2-24013300-C-G		not specified	Uncertain significance (Jan 23, 2023)
2-24013346-C-T		not specified	Uncertain significance (Jun 03, 2024)
2-24013394-T-G		not specified	Uncertain significance (Dec 14, 2022)
2-24016268-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-24016942-T-A		not specified	Uncertain significance (Oct 12, 2021)
2-24017308-C-G		not specified	Uncertain significance (May 05, 2022)
2-24017350-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-24017358-G-T		not specified	Uncertain significance (Feb 06, 2024)
2-24017499-G-A		not specified	Uncertain significance (Oct 25, 2022)
2-24017520-G-A		not specified	Uncertain significance (Jul 12, 2023)
2-24017523-G-A		not specified	Uncertain significance (Aug 17, 2021)
2-24017528-C-A		not specified	Uncertain significance (Oct 27, 2022)
2-24021655-T-C		not specified	Uncertain significance (Jun 03, 2022)
2-24021667-C-T		not specified	Uncertain significance (Jan 18, 2023)
2-24021675-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-24021732-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-24022454-C-G		not specified	Uncertain significance (Jan 26, 2022)
2-24022514-C-G		not specified	Uncertain significance (May 20, 2024)
2-24022883-C-T		not specified	Likely benign (Jul 25, 2023)
2-24023139-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-24023190-G-A		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD2B	protein_coding	protein_coding	ENST00000406420	13	53241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.33e-11	0.231	124698	0	83	124781	0.000333

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.226	274	285	0.962	0.0000166	3099
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000781	0.000764
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.00173	0.00173
Finnish	0.000420	0.000371
European (Non-Finnish)	0.000169	0.000168
Middle Eastern	0.00173	0.00173
South Asian	0.0000985	0.0000980
Other	0.000339	0.000330

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.275
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfsd2b
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: lipid transport;carbohydrate transport;transmembrane transport;organic substance transport
• Cellular component: integral component of plasma membrane
• Molecular function: transporter activity;symporter activity;sphingolipid transporter activity