NDRG1

protein-coding

N-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]

Previous symbols:
  • CAP43

MANE transcript

NM_006096.4

Inheritance

AR

ClinVar variants

P:53U:267B:227

Top phenotype

Charcot-Marie-Tooth disease, type 4D

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr8:133,237,175-133,302,022

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~64.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Charcot-Marie-Tooth disease type 4DSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011085

Submitter: Labcorp Genetics (formerly Invitae)

Charcot-Marie-Tooth disease type 4DSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011085

Submitter: PanelApp Australia

Charcot-Marie-Tooth disease type 4DDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011085

Submitter: Illumina

Charcot-Marie-Tooth disease type 4DSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011085

Submitter: Orphanet

Charcot-Marie-Tooth disease type 4DDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011085

Submitter: Natera

Clinical Genomic Database (CGD)

Charcot-Marie-Tooth disease, type 4DAR

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

Refs: 10831399; 22978647; 23163601; 24136616Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NDRG1 variants in ClinVar

7 Conditions Cataloged
Charcot-Marie-Tooth disease type 4Total: 642
Charcot-Marie-Tooth disease type 4DTotal: 168
not providedTotal: 132
Inborn genetic diseasesTotal: 109
not specifiedTotal: 52
Charcot-Marie-Tooth diseaseTotal: 48
NDRG1-related disorderTotal: 47

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
215
clinvar
2
clinvar
222
missense
242
clinvar
8
clinvar
1
clinvar
251
nonsense
7
clinvar
7
clinvar
1
clinvar
15
start loss
0
frameshift
5
clinvar
7
clinvar
6
clinvar
18
splice donor/acceptor (+/-2bp)
5
clinvar
22
clinvar
13
clinvar
1
clinvar
41
Total17362672243547

Highest pathogenic variant AF is 0.000011169662

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006096.4RefSeqNP_006087.215MANE Select
ENST00000323851.13EnsemblENSP00000319977.815MANE Select
NM_001135242.2RefSeqNP_001128714.115Standard
NM_001258432.2RefSeqNP_001245361.113Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ndrg1bDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6512262550.8850.00001682579
Missense (PolyPhen)88109.670.802381081
Synonymous-0.6641101011.080.00000744763
Loss of Function3.14824.90.3220.00000127271

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000110.00011rare
Finnish0.000790.00065rare
European (Non-Finnish)0.0000970.000079rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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