NIPAL2
protein-codingNIPA like domain containing 2, the group of Solute carrier family 57, NIPA-like magnesium transporters
Gene summary
Predicted to enable magnesium ion transmembrane transporter activity. Predicted to be involved in magnesium ion transport. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- NPAL2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~104.6 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 NIPAL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001321635.2. 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 | 2 | 2 | ||||
| missense | 45 | 1 | 46 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 52 | 1 | 0 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001308564.1 | 11 | MANE Select | |
| Ensembl | ENSP00000407087.2 | 11 | MANE Select | |
| RefSeq | NP_001308565.1 | 10 | Standard | |
| RefSeq | NP_079035.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Transport of small molecules
- Miscellaneous transport and binding events
Biological Process
- magnesium ion transport
- magnesium ion transmembrane transport
Molecular Function
- magnesium ion transmembrane transporter activity
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000341166
- Coding exons
- 12
- Length
- 104561
- Individuals with no LoFs
- 26927
- Homozygous LoFs
- 37563
- Heterozygous LoFs
- 61258
- Defined
- 125748
- p
- 0.537
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.810 | 149 | 180 | 0.830 | 0.00000870 | 2352 |
| Missense (PolyPhen) | 49 | 62.034 | 0.78989 | 830 | ||
| Synonymous | 0.748 | 60 | 67.8 | 0.884 | 0.00000361 | 728 |
| Loss of Function | 0.187 | 18 | 18.9 | 0.954 | 8.57e-7 | 249 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.52 | 0.52 | notable |
| Latino/Admixed American | 0.64 | 0.63 | notable |
| Ashkenazi Jewish | 0.56 | 0.55 | notable |
| East Asian | 0.59 | 0.60 | notable |
| Finnish | 0.51 | 0.51 | notable |
| European (Non-Finnish) | 0.50 | 0.50 | notable |
| South Asian | 0.61 | 0.60 | notable |
| Other | 0.54 | 0.54 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.408
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 67.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00412
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |