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MFSD3

Chr 8

solute carrier family 33 member 2

Also known as: MFSD3

NCBI Gene: 113655 UniProt: Q96ES6 OMIM: 620308

The protein functions as a transmembrane transporter involved in moving substances across cellular membranes. Mutations cause autosomal recessive developmental and epileptic encephalopathy with microcephaly, typically presenting in early infancy with severe intellectual disability, seizures, and brain malformations. The gene shows minimal constraint against loss-of-function variants, which is consistent with the recessive inheritance pattern observed in affected patients.

OMIM ResearchSummary from RefSeq

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.85

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

ensembl: Error: Ensembl fetch failed: 400 for /lookup/symbol/homo_sapiens/MFSD3?content-type=application/json

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.85LOEUF

pLI 0.000

Z-score -0.95

OE 1.30 (0.86–1.85)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.39Z-score

OE missense 1.27 (1.15–1.41)

264 obs / 207.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.30 (0.86–1.85)

0≤0.351.4

Missense OE?1.27 (1.15–1.41)

0≤0.61.4

Synonymous OE?1.38

0≤1.21.6

LoF obs/exp: 15 / 11.5Missense obs/exp: 264 / 207.5Syn Z: -3.18

Background carrier burden — how many people carry a rare variant somewhere in MFSD3?

gnomAD v4 · ~730k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 60

733 rare PASS variants

Rare truncating (LoF)

1 in 600

139 rare PASS variants

Rare synonymous (reference)

1 in 84

398 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MFSD3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 100	1 in 1,100
South Asian	~43k	1 in 85	1 in 1,000
Remaining (unassigned)	~30k	1 in 66	1 in 330
European (Finnish)	~26k	1 in 150	1 in 1,600
Admixed American	~22k	1 in 71	1 in 590
African / African American	~21k	1 in 63	1 in 360
East Asian	~20k	1 in 82	1 in 350
Ashkenazi Jewish	~13k	1 in 610	≈ 1 in 2,600
Middle Eastern	~2,884	1 in 73	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.