NMRK1

nicotinamide riboside kinase 1

Basic information

Region (hg38): 9:75060573-75088217

Previous symbols: [ "C9orf95" ]

Links

ENSG00000106733 ∙ NCBI:54981 ∙ OMIM:608704 ∙ HGNC:26057 ∙ Uniprot:Q9NWW6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NMRK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMRK1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in NMRK1

This is a list of pathogenic ClinVar variants found in the NMRK1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-75066808-G-A		not specified	Uncertain significance (Aug 20, 2023)
9-75069086-G-A		not specified	Uncertain significance (Jun 23, 2023)
9-75069091-T-C		not specified	Uncertain significance (Aug 12, 2024)
9-75069747-C-A		not specified	Uncertain significance (Jul 15, 2024)
9-75069750-C-G		not specified	Uncertain significance (Sep 22, 2022)
9-75069769-G-A		not specified	Uncertain significance (Jun 07, 2024)
9-75069775-G-A		not specified	Uncertain significance (Sep 12, 2024)
9-75069898-T-A		not specified	Uncertain significance (Feb 10, 2022)
9-75069922-A-G		not specified	Uncertain significance (Apr 25, 2023)
9-75069927-T-G		not specified	Uncertain significance (Feb 04, 2025)
9-75069946-G-A		not specified	Uncertain significance (Oct 01, 2024)
9-75069950-T-C		not specified	Uncertain significance (Oct 16, 2024)
9-75069968-C-G		not specified	Uncertain significance (May 25, 2022)
9-75077160-A-T		not specified	Uncertain significance (Feb 10, 2025)
9-75077162-C-T		not specified	Uncertain significance (Sep 03, 2024)
9-75077166-C-G		not specified	Uncertain significance (Oct 20, 2024)
9-75077189-T-C		not specified	Uncertain significance (Oct 27, 2022)
9-75077507-G-C		not specified	Uncertain significance (Apr 08, 2024)
9-75077517-A-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMRK1	protein_coding	protein_coding	ENST00000361092	8	27645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.57e-8	0.193	125582	0	165	125747	0.000656

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.328	93	102	0.909	0.00000465	1328
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00518	0.00519
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000527	0.000523
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;Metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.23

Haploinsufficiency Scores

• pHI: 0.0663
• hipred: N
• hipred_score: 0.216
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nmrk1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: UMP biosynthetic process;NAD biosynthetic process;phosphorylation;NAD metabolic process
• Cellular component: cytosol
• Molecular function: protein binding;ATP binding;kinase activity;metal ion binding;ribosylnicotinamide kinase activity;ribosylnicotinate kinase activity