NME5
NME/NM23 family member 5, the group of NME/NM23 family
Basic information
Region (hg38): 5:138115174-138139443
Links
Phenotypes
GenCC
Source:
- ciliary dyskinesia, primary, 48, without situs inversus (Limited), mode of inheritance: AR
- ciliary dyskinesia, primary, 48, without situs inversus (Limited), mode of inheritance: Unknown
- ciliary dyskinesia, primary, 48, without situs inversus (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ciliary dyskinesia, primary, 48 without situs inversus | AR | Allergy/Immunology/Infectious; Pulmonary | Pulmonary surveillance may be beneficial to assess respiratory function and institute early management measures, and early and aggressive treatment of respiratory infections may be beneficial | Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Pulmonary | 31479451; 32185794; 32950024 |
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 NME5 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 | 8 | |||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 1 | 9 | 0 | 0 |
Variants in NME5
This is a list of pathogenic ClinVar variants found in the NME5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-138115745-AG-A | Ciliary dyskinesia, primary, 48, without situs inversus | Uncertain significance (Mar 29, 2024) | ||
| 5-138115748-C-T | Ciliary dyskinesia, primary, 48, without situs inversus | Likely pathogenic (Feb 23, 2023) | ||
| 5-138115749-A-G | not specified | Uncertain significance (Dec 21, 2023) | ||
| 5-138128499-AT-A | Ciliary dyskinesia, primary, 48, without situs inversus | Pathogenic (Sep 15, 2022) | ||
| 5-138128514-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 5-138129289-T-G | not specified | Uncertain significance (Jul 06, 2021) | ||
| 5-138129305-C-G | not specified | Uncertain significance (May 26, 2024) | ||
| 5-138129338-T-C | not specified | Uncertain significance (Jan 04, 2022) | ||
| 5-138129450-T-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 5-138129453-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
| 5-138129456-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 5-138138678-G-T | not specified | Uncertain significance (Dec 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NME5 | protein_coding | protein_coding | ENST00000265191 | 5 | 24267 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000672 | 0.759 | 125720 | 0 | 23 | 125743 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.414 | 103 | 116 | 0.892 | 0.00000562 | 1399 |
| Missense in Polyphen | 32 | 39.394 | 0.81231 | 474 | ||
| Synonymous | 1.86 | 23 | 37.4 | 0.614 | 0.00000190 | 391 |
| Loss of Function | 0.981 | 6 | 9.21 | 0.651 | 3.86e-7 | 127 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000255 | 0.000254 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000132 | 0.000132 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Does not seem to have NDK kinase activity. Confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. May play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species (By similarity). {ECO:0000250}.;
- Pathway
- pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;UTP and CTP <i>de novo</i> biosynthesis;Folate metabolism;purine deoxyribonucleosides salvage;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)
Intolerance Scores
- loftool
- 0.715
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 72.01
Haploinsufficiency Scores
- pHI
- 0.166
- hipred
- Y
- hipred_score
- 0.680
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.163
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nme5
- Phenotype
- cellular phenotype; craniofacial phenotype; skeleton phenotype; immune system 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); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype;
Gene ontology
- Biological process
- epithelial cilium movement;nucleoside diphosphate phosphorylation;GTP biosynthetic process;UTP biosynthetic process;CTP biosynthetic process;spermatogenesis;spermatid development;nucleoside metabolic process;ventricular system development;cilium assembly;negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
- Cellular component
- cellular_component;sperm flagellum
- Molecular function
- nucleoside diphosphate kinase activity;protein binding