MFSD6

protein-coding

major facilitator superfamily domain containing 6

Gene summary

Predicted to enable MHC class I protein binding activity and MHC class I receptor activity. Predicted to be involved in antigen processing and presentation of exogenous peptide antigen via MHC class I. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017694.4

Inheritance

—

ClinVar variants

U:99B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr2:190,408,355-190,509,205

External References & Databases

Ensembl (ENSG00000151690)

Transcript & Mutation Effects

hg38 • Region Span ~100.9 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 MFSD6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017694.4. 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			4 clinvar		3 clinvar	7
missense			95 clinvar	2 clinvar	1 clinvar	98
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	99	2	4	105

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017694.4	RefSeq	NP_060164.3	6	MANE Select
ENST00000392328.6	Ensembl	ENSP00000376141.1	6	MANE Select
NM_001375986.1	RefSeq	NP_001362915.1	6	Standard
NM_001375987.1	RefSeq	NP_001362916.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392328
Coding exons: 6
Length: 100851
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125748
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.77	335	440	0.762	0.0000247	5170
Missense (PolyPhen)		57	121.41	0.46946		1485
Synonymous	-0.461	176	168	1.05	0.0000103	1612
Loss of Function	2.24	13	25.1	0.517	0.00000117	320

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00023	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.500
RVIS EVS: 0.51
RVIS percentile EVS: 80.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0229

Gene Damage Prediction

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