NDRG1
protein-codingN-myc downstream regulated 1, the group of NDRG family
Gene summary
This gene is a member of the N-myc downregulated gene family which belongs to the alpha/beta hydrolase superfamily. The protein encoded by this gene is a cytoplasmic protein involved in stress responses, hormone responses, cell growth, and differentiation. The encoded protein is necessary for p53-mediated caspase activation and apoptosis. Mutations in this gene are a cause of Charcot-Marie-Tooth disease type 4D, and expression of this gene may be a prognostic indicator for several types of cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
- CAP43
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~64.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0011085
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0011085
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011085
Submitter: Illumina
Inheritance Pattern: AR
Disease ID:MONDO:0011085
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0011085
Submitter: Natera
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NDRG1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006096.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 215 | 2 | 222 | ||
| missense | 242 | 8 | 1 | 251 | ||
| nonsense | 7 | 7 | 1 | 15 | ||
| start loss | 0 | |||||
| frameshift | 5 | 7 | 6 | 18 | ||
| splice donor/acceptor (+/-2bp) | 5 | 22 | 13 | 1 | 41 | |
| Total | 17 | 36 | 267 | 224 | 3 | 547 |
Highest pathogenic variant AF is 0.000011169662
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006087.2 | 15 | MANE Select | |
| Ensembl | ENSP00000319977.8 | 15 | MANE Select | |
| RefSeq | NP_001128714.1 | 15 | Standard | |
| RefSeq | NP_001245361.1 | 13 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ndrg1b | Danio rerio | Structure: thymus Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Androgen Receptor Network in Prostate Cancer
- TP53 Regulates Transcription of Cell Death Genes
- VEGFA-VEGFR2 Signaling Pathway
- Gene expression (Transcription)
- Generic Transcription Pathway
Biological Process
- signal transduction
- negative regulation of cell population proliferation
- response to metal ion
- DNA damage response, signal transduction by p53 class mediator
- peripheral nervous system myelin maintenance
Molecular Function
- protein binding
- microtubule binding
- Rab GTPase binding
- gamma-tubulin binding
- cadherin binding
Cellular Component
- nucleus
- cytoplasm
- centrosome
- cytosol
- microtubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000414097
- Coding exons
- 15
- Length
- 64852
- Individuals with no LoFs
- 125718
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 29
- Defined
- 125748
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.651 | 226 | 255 | 0.885 | 0.0000168 | 2579 |
| Missense (PolyPhen) | 88 | 109.67 | 0.80238 | 1081 | ||
| Synonymous | -0.664 | 110 | 101 | 1.08 | 0.00000744 | 763 |
| Loss of Function | 3.14 | 8 | 24.9 | 0.322 | 0.00000127 | 271 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00079 | 0.00065 | rare |
| European (Non-Finnish) | 0.000097 | 0.000079 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Stress-responsive protein involved in hormone responses, cell growth, and differentiation. Acts as a tumor suppressor in many cell types. Necessary but not sufficient for p53/TP53- mediated caspase activation and apoptosis. Has a role in cell trafficking, notably of the Schwann cell, and is necessary for the maintenance and development of the peripheral nerve myelin sheath. Required for vesicular recycling of CDH1 and TF. May also function in lipid trafficking. Protects cells from spindle disruption damage. Functions in p53/TP53-dependent mitotic spindle checkpoint. Regulates microtubule dynamics and maintains euploidy. {ECO:0000269|PubMed:15247272, ECO:0000269|PubMed:15377670, ECO:0000269|PubMed:17786215, ECO:0000269|PubMed:9766676}.;
- Disease
- DISEASE: Charcot-Marie-Tooth disease 4D (CMT4D) [MIM:601455]: A recessive demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. By convention autosomal recessive forms of demyelinating Charcot-Marie-Tooth disease are designated CMT4. {ECO:0000269|PubMed:10831399}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.381
Intolerance Scores
- LoFtool
- 0.732
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.71
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |