NME3
NME/NM23 nucleoside diphosphate kinase 3, the group of NME/NM23 family
Basic information
Region (hg38): 16:1770320-1771561
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 14 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 14 | 1 | 1 |
Variants in NME3
This is a list of pathogenic ClinVar variants found in the NME3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-1770682-C-T | NME3-related condition | Likely benign (Aug 20, 2024) | ||
| 16-1770690-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 16-1770725-C-T | not specified | Uncertain significance (Dec 07, 2021) | ||
| 16-1770729-G-A | not specified | Uncertain significance (Sep 30, 2024) | ||
| 16-1770766-C-T | not specified | Likely benign (Mar 07, 2025) | ||
| 16-1770884-C-A | not specified | Uncertain significance (Sep 04, 2024) | ||
| 16-1770891-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 16-1770920-G-C | not specified | Uncertain significance (May 17, 2023) | ||
| 16-1770962-G-A | not specified | Uncertain significance (Jan 08, 2024) | ||
| 16-1770976-G-C | not specified | Uncertain significance (Jun 07, 2024) | ||
| 16-1770986-T-G | not specified | Uncertain significance (Nov 10, 2024) | ||
| 16-1771083-G-A | not specified | Uncertain significance (Aug 12, 2024) | ||
| 16-1771125-C-T | not specified | Uncertain significance (Feb 26, 2025) | ||
| 16-1771246-ACACCGCGCCCCCGCTCGCT-A | not specified | Likely benign (Jan 06, 2020) | ||
| 16-1771330-G-A | Benign (Jul 13, 2018) | |||
| 16-1771345-C-T | not specified | Uncertain significance (Nov 18, 2023) | ||
| 16-1771371-T-G | not specified | Uncertain significance (Nov 14, 2023) | ||
| 16-1771506-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 16-1771515-G-A | not specified | Conflicting classifications of pathogenicity (Aug 02, 2021) | ||
| 16-1771522-C-G | not specified | Uncertain significance (Nov 10, 2024) | ||
| 16-1771534-T-C | Uncertain significance (Jul 17, 2020) |
GnomAD
Source:
| 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:
- 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