MFSD1

protein-coding

major facilitator superfamily domain containing 1

Gene summary

Enables dipeptide uniporter activity. Involved in dipeptide transmembrane transport from lysosomal lumen to cytosol. Is active in lysosomal membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_022736.4

Inheritance

—

ClinVar variants

U:86B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr3:158,732,198-158,829,719

External References & Databases

Ensembl (ENSG00000118855)

Transcript & Mutation Effects

hg38 • Region Span ~97.5 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 MFSD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 72

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022736.4. 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				2 clinvar		2
missense			77 clinvar	1 clinvar		78
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	86	3	0	89

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022736.4	RefSeq	NP_073573.3	16	MANE Select
ENST00000415822.8	Ensembl	ENSP00000403117.3	16	MANE Select
NM_001167903.3	RefSeq	NP_001161375.2	15	Standard
NM_001289406.3	RefSeq	NP_001276335.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transmembrane transport

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000415822
Coding exons: 16
Length: 97522
Individuals with no LoFs: 125595
Homozygous LoFs: 0
Heterozygous LoFs: 153
Defined: 125748
p: 0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0244	280	279	1.00	0.0000132	3315
Missense (PolyPhen)		49	50.256	0.97501		582
Synonymous	-0.923	117	105	1.11	0.00000514	1021
Loss of Function	0.476	27	29.8	0.906	0.00000154	341

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.00044	0.00044	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00074	0.00074	rare
South Asian	0.00030	0.00029	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.804
RVIS EVS: 0.2
RVIS percentile EVS: 67.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.574

Gene Damage Prediction

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