NME6
NME/NM23 nucleoside diphosphate kinase 6, the group of NME/NM23 family
Basic information
Region (hg38): 3:48290722-48301685
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 NME6 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 | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 13 | 1 | 0 |
Variants in NME6
This is a list of pathogenic ClinVar variants found in the NME6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-48294645-G-A | not specified | Uncertain significance (Dec 12, 2023) | ||
| 3-48294692-C-A | not specified | Uncertain significance (Sep 26, 2022) | ||
| 3-48294695-T-C | not specified | Uncertain significance (Jan 24, 2023) | ||
| 3-48294701-A-G | not specified | Uncertain significance (Feb 27, 2023) | ||
| 3-48294744-G-A | not specified | Uncertain significance (Nov 15, 2024) | ||
| 3-48295092-T-G | not specified | Uncertain significance (Jan 19, 2025) | ||
| 3-48295108-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
| 3-48295122-C-T | not specified | Uncertain significance (Mar 09, 2025) | ||
| 3-48295129-A-T | not specified | Uncertain significance (Dec 30, 2024) | ||
| 3-48295152-C-A | not specified | Uncertain significance (Jan 22, 2025) | ||
| 3-48295161-C-G | not specified | Uncertain significance (Feb 27, 2023) | ||
| 3-48295188-A-G | not specified | Uncertain significance (Aug 05, 2024) | ||
| 3-48295224-C-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 3-48296122-G-T | not specified | Uncertain significance (Oct 29, 2024) | ||
| 3-48296738-C-T | not specified | Likely benign (Jun 25, 2024) | ||
| 3-48296757-C-A | not specified | Uncertain significance (Nov 20, 2024) | ||
| 3-48296786-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 3-48298521-C-G | not specified | Uncertain significance (Dec 13, 2023) | ||
| 3-48301594-C-CCCCTCGGAAGCCGGCCTGGGCGCCCTCGGAAGCCGGCCTGGGCGCCCTCGGAAGCCGGCCTGGGCG | Likely benign (Apr 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NME6 | protein_coding | protein_coding | ENST00000421967 | 6 | 8422 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.27e-7 | 0.387 | 125683 | 0 | 65 | 125748 | 0.000258 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.261 | 109 | 117 | 0.932 | 0.00000689 | 1244 |
| Missense in Polyphen | 39 | 47.682 | 0.81793 | 450 | ||
| Synonymous | 1.40 | 29 | 40.3 | 0.720 | 0.00000205 | 387 |
| Loss of Function | 0.603 | 11 | 13.4 | 0.822 | 0.00000100 | 108 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000518 | 0.000517 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00165 | 0.00163 |
| Finnish | 0.000232 | 0.000231 |
| European (Non-Finnish) | 0.000123 | 0.000123 |
| Middle Eastern | 0.00165 | 0.00163 |
| South Asian | 0.000170 | 0.000163 |
| Other | 0.00 | 0.00 |
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. Inhibitor of p53-induced apoptosis.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Pyrimidine Metabolism;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;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
- 0.0929
Intolerance Scores
- loftool
- 0.819
- rvis_EVS
- -0.41
- rvis_percentile_EVS
- 26.23
Haploinsufficiency Scores
- pHI
- 0.0813
- hipred
- Y
- hipred_score
- 0.550
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nme6
- Phenotype
- 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); growth/size/body region phenotype; 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); embryo phenotype;
Gene ontology
- Biological process
- nucleoside diphosphate phosphorylation;GTP biosynthetic process;UTP biosynthetic process;CTP biosynthetic process;apoptotic process;negative regulation of cell growth;negative regulation of mitotic nuclear division
- Cellular component
- mitochondrion
- Molecular function
- nucleoside diphosphate kinase activity;protein binding;ATP binding;metal ion binding