NME1

NME/NM23 nucleoside diphosphate kinase 1, the group of NME/NM23 family|SET complex

Basic information

Region (hg38): 17:51153559-51162428

Links

ENSG00000239672

∙ NCBI:4830 ∙ OMIM:156490 ∙ HGNC:7849 ∙ Uniprot:P15531 ∙ 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 NME1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NME1 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 clinvar		1
missense			1 clinvar	1 clinvar		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4 clinvar	4
Total	0	0	1	2	4

Variants in NME1

This is a list of pathogenic ClinVar variants found in the NME1 region.

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

Position	Phenotype	Significance	ClinVar
17-51154262-C-G	not specified	Benign (Jan 24, 2024)	2688272
17-51154266-G-A	not specified	Benign (Jan 24, 2024)	2688150
17-51154423-CT-C		Uncertain significance (-)	1049321
17-51155675-C-A	NME1-NME2-related disorder	Likely benign (Aug 14, 2019)	3052782
17-51161282-T-G	NME1-NME2-related disorder	Benign (May 14, 2018)	727415
17-51161675-C-A	not specified	Benign (Jan 24, 2024)	2688180
17-51161814-C-T	not specified	Likely benign (Jul 19, 2023)	2592832
17-51161838-A-G	not specified	Uncertain significance (Jul 06, 2021)	2234604

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NME1	protein_coding	protein_coding	ENST00000336097	5	8893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00318	0.835	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.537	92	108	0.854	0.00000670	1155
Missense in Polyphen		22	33.924	0.64851		424
Synonymous	0.342	37	39.7	0.931	0.00000247	339
Loss of Function	1.16	5	8.70	0.575	4.56e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000309	0.0000309
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000352
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein- coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination. During GZMA-mediated cell death, works in concert with TREX1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair. {ECO:0000269|PubMed:12628186, ECO:0000269|PubMed:16818237, ECO:0000269|PubMed:8810265}.;
Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Tenofovir/Adefovir Pathway, Pharmacodynamics;Tenofovir/Adefovir Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Abacavir Pathway, Pharmacokinetics/Pharmacodynamics;Adefovir Dipivoxil Metabolism Pathway;Tenofovir Metabolism Pathway;Gemcitabine Action Pathway;Lamivudine Metabolism Pathway;Gemcitabine Metabolism Pathway;Pyrimidine metabolism;pyrimidine deoxyribonucleotides de novo biosynthesis;UTP and CTP de novo biosynthesis;granzyme a mediated apoptosis pathway;endocytotic role of ndk phosphins and dynamin;Metabolism of nucleotides;Folate metabolism;purine deoxyribonucleosides salvage;Interconversion of nucleotide di- and triphosphates;Purine metabolism;Metabolism;Pyrimidine metabolism;superpathway of pyrimidine ribonucleotides de novo biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;TGF_beta_Receptor;Purine nucleotides nucleosides metabolism;CMP phosphorylation;superpathway of purine nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;Posttranslational regulation of adherens junction stability and dissassembly;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP;Arf6 trafficking events;guanosine deoxyribonucleotides de novo biosynthesis;guanosine nucleotides de novo biosynthesis;adenosine deoxyribonucleotides de novo biosynthesis;guanosine ribonucleotides de novo biosynthesis;purine nucleotides de novo biosynthesis;Regulation of CDC42 activity;Validated targets of C-MYC transcriptional activation;Arf6 downstream pathway;E-cadherin signaling in the nascent adherens junction (Consensus)

Recessive Scores

pRec: 0.461

Intolerance Scores

loftool: 0.866
rvis_EVS: -0.12
rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

pHI
hipred: Y
hipred_score: 0.506
ghis: 0.464

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nme1
Phenotype: liver/biliary system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process: negative regulation of myeloid leukocyte differentiation;nucleoside diphosphate phosphorylation;GTP biosynthetic process;UTP biosynthetic process;CTP biosynthetic process;DNA metabolic process;endocytosis;lactation;negative regulation of cell population proliferation;negative regulation of gene expression;positive regulation of neuron projection development;response to amine;nucleobase-containing small molecule interconversion;hippocampus development;response to testosterone;cellular response to drug;regulation of apoptotic process;positive regulation of DNA binding;positive regulation of epithelial cell proliferation;response to cAMP;cellular response to glucose stimulus;cellular response to fatty acid
Cellular component: nucleus;cytoplasm;mitochondrial outer membrane;centrosome;cytosol;intermediate filament;membrane;ruffle membrane;myelin sheath;perinuclear region of cytoplasm;extracellular exosome
Molecular function: magnesium ion binding;RNA polymerase II regulatory region sequence-specific DNA binding;single-stranded DNA binding;RNA binding;deoxyribonuclease activity;nucleoside diphosphate kinase activity;protein binding;ATP binding;GTP binding;intermediate filament binding;enzyme binding;identical protein binding;gamma-tubulin binding;ribosomal small subunit binding