MLANA
protein-codingmelan-A
Gene summary
Located in endoplasmic reticulum membrane; melanosome; and trans-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.7 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 MLANA variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005511.2. 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 | 0 | |||||
| missense | 17 | 1 | 18 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 1 | 3 | |||
| Total | 0 | 0 | 19 | 2 | 0 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005502.1 | 4 | MANE Select | |
| Ensembl | ENSP00000370886.3 | 4 | MANE Select | |
| Ensembl | ENSP00000370880.1 | 4 | Standard | |
| Ensembl | ENSP00000370880.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- endoplasmic reticulum membrane
- Golgi apparatus
- trans-Golgi network
- integral component of plasma membrane
- melanosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381477
- Coding exons
- 4
- Length
- 19805
- Individuals with no LoFs
- 125408
- Homozygous LoFs
- 8
- Heterozygous LoFs
- 312
- Defined
- 125728
- p
- 0.00127
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.119 | 67 | 64.3 | 1.04 | 0.00000338 | 746 |
| Missense (PolyPhen) | 16 | 17.119 | 0.93465 | 193 | ||
| Synonymous | -0.515 | 27 | 23.8 | 1.13 | 0.00000132 | 232 |
| Loss of Function | -1.65 | 11 | 6.46 | 1.70 | 3.71e-7 | 78 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.0017 | 0.0016 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.014 | 0.014 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000072 | 0.000070 | rare |
| South Asian | 0.00013 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in melanosome biogenesis by ensuring the stability of GPR143. Plays a vital role in the expression, stability, trafficking, and processing of melanocyte protein PMEL, which is critical to the formation of stage II melanosomes. {ECO:0000269|PubMed:15695812, ECO:0000269|PubMed:19717472}.;
Recessive Scores
- pRec
- 0.376
Intolerance Scores
- LoFtool
- 0.508
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.86
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.641
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |