MFSD12
protein-codingmajor facilitator superfamily domain containing 12
Gene summary
Enables cysteine transmembrane transporter activity. Involved in cysteine transmembrane transport; pigment metabolic process involved in pigmentation; and regulation of melanin biosynthetic process. Located in lysosome and melanosome. Part of late endosome. [provided by Alliance of Genome Resources, Jul 2025]
- C19orf28
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.0 kbGenCC 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 MFSD12 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_174983.5. 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 | 3 | 1 | 1 | 5 | ||
| missense | 6 | 2 | 8 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 15 | 3 | 1 | 19 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_778148.2 | 10 | MANE Select | |
| Ensembl | ENSP00000347583.1 | 10 | MANE Select | |
| RefSeq | NP_001274458.1 | 10 | Standard | |
| Ensembl | ENSP00000381566.4 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mfsd12a | Danio rerio | Structure: xanthophore Quality: disrupted abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- carbohydrate transport
- transmembrane transport
- organic substance transport
Molecular Function
- transporter activity
- symporter activity
Cellular Component
- lysosomal membrane
- integral component of plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000398558
- Coding exons
- 10
- Length
- 36030
- Individuals with no LoFs
- 124628
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 218
- Defined
- 124846
- p
- 0.000873
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.74 | 459 | 321 | 1.43 | 0.0000197 | 3348 |
| Missense (PolyPhen) | 151 | 105.14 | 1.4362 | 1143 | ||
| Synonymous | -3.91 | 214 | 153 | 1.40 | 0.0000106 | 1155 |
| Loss of Function | -0.115 | 26 | 25.4 | 1.02 | 0.00000133 | 256 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00026 | rare |
| Latino/Admixed American | 0.00050 | 0.00049 | rare |
| Ashkenazi Jewish | 0.0083 | 0.0083 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00080 | 0.00078 | rare |
| South Asian | 0.00056 | 0.00056 | rare |
| Other | 0.00067 | 0.00066 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- -0.26
- RVIS percentile EVS
- 34.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |