NKPD1
protein-codingNTPase KAP family P-loop domain containing 1
Gene summary
Predicted to be located in membrane. [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 ~11.2 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 NKPD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198478.4. 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 | 0 | |||||
| missense | 143 | 11 | 154 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 143 | 11 | 0 | 154 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940880.3 | 4 | MANE Select | |
| Ensembl | ENSP00000509174.1 | 4 | MANE Select | |
| Ensembl | ENSP00000321976.6 | 4 | Standard | |
| Ensembl | ENSP00000321976.6 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000317951
- Coding exons
- 4
- Length
- 10401
- Individuals with no LoFs
- 123321
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 97
- Defined
- 123418
- p
- 0.000393
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.24 | 341 | 479 | 0.712 | 0.0000306 | 5194 |
| Missense (PolyPhen) | 96 | 161.66 | 0.59384 | 1785 | ||
| Synonymous | 1.81 | 196 | 231 | 0.849 | 0.0000163 | 1771 |
| Loss of Function | 1.66 | 13 | 21.3 | 0.611 | 0.00000109 | 233 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0019 | 0.0015 | notable |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00033 | 0.00030 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00044 | 0.00037 | rare |
| European (Non-Finnish) | 0.00062 | 0.00051 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0.00057 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
Essentials
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.482
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |