NMRK1
protein-codingnicotinamide riboside kinase 1
Gene summary
Nicotinamide adenine dinucleotide (NAD+) is essential for life in all organisms, both as a coenzyme for oxidoreductases and as a source of ADP-ribosyl groups used in various reactions. Nicotinic acid and nicotinamide, collectively known as niacin, are the vitamin precursors of NAD+. Nicotinamide riboside kinases, such as NRK1, function to synthesize NAD+ through nicotinamide mononucleotide using nicotinamide riboside as the precursor (Bieganowski and Brenner, 2004 [PubMed 15137942]).[supplied by OMIM, Mar 2008]
- C9orf95
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0007661
Submitter: Labcorp Genetics (formerly Invitae)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NMRK1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017881.3. 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 | 1 | 1 | ||||
| missense | 33 | 33 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 36 | 0 | 0 | 36 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060351.1 | 8 | MANE Select | |
| Ensembl | ENSP00000354387.4 | 8 | MANE Select | |
| RefSeq | NP_001121075.1 | 7 | Standard | |
| RefSeq | NP_001317607.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nicotinate and nicotinamide metabolism - Homo sapiens (human)
- Nicotinate and Nicotinamide Metabolism
- Metabolism
- Nicotinate metabolism
- Metabolism of water-soluble vitamins and cofactors
Biological Process
- UMP biosynthetic process
- NAD biosynthetic process
- phosphorylation
- NAD metabolic process
Molecular Function
- protein binding
- ATP binding
- kinase activity
- metal ion binding
- ribosylnicotinamide kinase activity
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361092
- Coding exons
- 8
- Length
- 27645
- Individuals with no LoFs
- 125582
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 165
- Defined
- 125747
- p
- 0.000656
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.328 | 93 | 102 | 0.909 | 0.00000465 | 1328 |
| Missense (PolyPhen) | 33 | 37.043 | 0.89085 | 469 | ||
| Synonymous | 0.570 | 30 | 34.2 | 0.876 | 0.00000181 | 329 |
| Loss of Function | 0.260 | 12 | 13.0 | 0.922 | 5.52e-7 | 161 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00092 | 0.00092 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.0052 | 0.0052 | notable |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00053 | 0.00052 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the phosphorylation of nicotinamide riboside (NR) and nicotinic acid riboside (NaR) to form nicotinamide mononucleotide (NMN) and nicotinic acid mononucleotide (NaMN). The enzyme also phosphorylates the antitumor drugs tiazofurin and 3- deazaguanosine. {ECO:0000269|PubMed:15137942}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- RVIS EVS
- 0.84
- RVIS percentile EVS
- 88.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |