NMRK2

nicotinamide riboside kinase 2

Basic information

Region (hg38): 19:3933069-3942416

Previous symbols: [ "ITGB1BP3" ]

Links

ENSG00000077009 ∙ NCBI:27231 ∙ OMIM:608705 ∙ HGNC:17871 ∙ Uniprot:Q9NPI5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NMRK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMRK2 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					1	1
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in NMRK2

This is a list of pathogenic ClinVar variants found in the NMRK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3936598-C-T		not specified	Uncertain significance (Apr 13, 2022)
19-3938631-G-A		not specified	Uncertain significance (Oct 19, 2024)
19-3938641-G-A		not specified	Uncertain significance (Mar 11, 2022)
19-3938686-G-A		not specified	Uncertain significance (Sep 27, 2024)
19-3938694-C-T			Benign (May 07, 2018)
19-3938752-A-C		not specified	Uncertain significance (Jan 31, 2023)
19-3939915-G-C		not specified	Uncertain significance (Sep 14, 2021)
19-3939940-G-A		not specified	Uncertain significance (May 27, 2022)
19-3941076-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-3941091-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-3941130-T-G		not specified	Uncertain significance (Aug 11, 2022)
19-3941160-C-T		not specified	Uncertain significance (Oct 25, 2023)
19-3942103-T-C		not specified	Uncertain significance (Jul 02, 2024)
19-3942107-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-3942161-G-A		not specified	Uncertain significance (Sep 19, 2022)
19-3942214-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-3942218-G-T		not specified	Uncertain significance (Dec 21, 2022)
19-3942226-G-A		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMRK2	protein_coding	protein_coding	ENST00000168977	7	9314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.92e-12	0.00459	125338	2	406	125746	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.173	151	145	1.04	0.00000952	1481
Missense in Polyphen		34	33.296	1.0211		354
Synonymous	-0.828	71	62.7	1.13	0.00000472	433
Loss of Function	-1.48	15	9.96	1.51	4.24e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00157
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0110	0.0110
European (Non-Finnish)	0.00101	0.00101
Middle Eastern	0.000109	0.000109
South Asian	0.000198	0.000196
Other	0.00295	0.00294

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). Reduces laminin matrix deposition and cell adhesion to laminin, but not to fibronectin. Involved in the regulation of PXN at the protein level and of PXN tyrosine phosphorylation. May play a role in the regulation of terminal myogenesis. {ECO:0000269|PubMed:10613898, ECO:0000269|PubMed:15137942}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);Metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.471
• hipred: N
• hipred_score: 0.264
• ghis: 0.468

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: Nmrk2
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: NAD biosynthetic process;phosphorylation;NAD metabolic process;negative regulation of myoblast differentiation
• Cellular component: nucleoplasm;cytosol;plasma membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;ATP binding;metal ion binding;ribosylnicotinamide kinase activity;ribosylnicotinate kinase activity