NDRG2

protein-coding

NDRG family member 2, the group of MicroRNA protein coding host genes|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 that may play a role in neurite outgrowth. This gene may be involved in glioblastoma carcinogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]

MANE transcript

NM_001320329.2

Inheritance

—

ClinVar variants

U:48B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr14:21,016,763-21,070,872

External References & Databases

Ensembl (ENSG00000165795)

Transcript & Mutation Effects

hg38 • Region Span ~54.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NDRG2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001320329.2. 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			2 clinvar		1 clinvar	3
missense			41 clinvar	3 clinvar	1 clinvar	45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	48	3	2	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 330 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001320329.2	RefSeq	NP_001307258.1	15	MANE Select
ENST00000556147.6	Ensembl	ENSP00000451712.1	15	MANE Select
NM_001282211.2	RefSeq	NP_001269140.1	15	Standard
NM_001282212.2	RefSeq	NP_001269141.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Validated targets of C-MYC transcriptional repression

Biological Process

negative regulation of cytokine production
signal transduction
regulation of vascular endothelial growth factor production
Wnt signaling pathway
substantia nigra development

Molecular Function

molecular_function
protein binding

Cellular Component

nucleus
cytoplasm
Golgi apparatus
cytosol
growth cone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000556147
Coding exons: 15
Length: 54110
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125748
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.621	192	218	0.882	0.0000122	2387
Missense (PolyPhen)		69	99.26	0.69515		1030
Synonymous	-0.296	89	85.5	1.04	0.00000508	737
Loss of Function	2.52	12	25.8	0.465	0.00000126	288

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000059	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Contributes to the regulation of the Wnt signaling pathway. Down-regulates CTNNB1-mediated transcriptional activation of target genes, such as CCND1, and may thereby act as tumor suppressor. May be involved in dendritic cell and neuron differentiation. {ECO:0000269|PubMed:12845671, ECO:0000269|PubMed:16103061, ECO:0000269|PubMed:21247902}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.743
RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.192

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium