NME3

NME/NM23 nucleoside diphosphate kinase 3, the group of NME/NM23 family

Basic information

Region (hg38): 16:1770320-1771561

Links

ENSG00000103024 ∙ NCBI:4832 ∙ OMIM:601817 ∙ HGNC:7851 ∙ Uniprot:Q13232 ∙ 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 NME3 gene.

• not_specified (34 variants)
• not_provided (3 variants)
• NME3-related_condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NME3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002513.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			31	1	1	33
nonsense				1		1
start loss			1			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	3	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NME3	protein_coding	protein_coding	ENST00000219302	5	1445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.73e-8	0.0383	121544	0	27	121571	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.686	106	87.9	1.21	0.00000420	1043
Missense in Polyphen		45	39.009	1.1536		451
Synonymous	-1.76	53	39.0	1.36	0.00000209	339
Loss of Function	-1.45	9	5.37	1.68	2.30e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000696	0.0000654
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000574	0.0000558
Finnish	0.00	0.00
European (Non-Finnish)	0.000112	0.000102
Middle Eastern	0.0000574	0.0000558
South Asian	0.000447	0.000426
Other	0.000185	0.000168

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. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;UTP and CTP <i>de novo</i> biosynthesis;Metabolism of nucleotides;Folate metabolism;purine deoxyribonucleosides salvage;Interconversion of nucleotide di- and triphosphates;Metabolism;superpathway of pyrimidine ribonucleotides <i>de novo</i> biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;Purine nucleotides nucleosides metabolism;CMP phosphorylation;superpathway of purine nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP;guanosine deoxyribonucleotides <i>de novo</i> biosynthesis;guanosine nucleotides <i>de novo</i> biosynthesis;adenosine deoxyribonucleotides <i>de novo</i> biosynthesis;guanosine ribonucleotides <i>de novo</i> biosynthesis;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.185

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.591
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.711

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nme3
• Phenotype: reproductive system phenotype

Zebrafish Information Network

• Gene name: nme3
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: nucleoside diphosphate phosphorylation;GTP biosynthetic process;UTP biosynthetic process;CTP biosynthetic process;apoptotic process;nucleobase-containing small molecule interconversion
• Cellular component: cytosol
• Molecular function: nucleoside diphosphate kinase activity;protein binding;ATP binding;metal ion binding