NDRG2

NDRG family member 2, the group of MicroRNA protein coding host genes|NDRG family

Basic information

Region (hg38): 14:21016763-21070872

Links

ENSG00000165795 ∙ NCBI:57447 ∙ OMIM:605272 ∙ HGNC:14460 ∙ Uniprot:Q9UN36 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDRG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDRG2 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					1	1
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	1	2

Variants in NDRG2

This is a list of pathogenic ClinVar variants found in the NDRG2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-21017625-G-A		not specified	Uncertain significance (Sep 17, 2021)
14-21017625-G-T		not specified	Uncertain significance (Apr 23, 2024)
14-21017636-G-A		not specified	Uncertain significance (Feb 05, 2024)
14-21017687-T-C		not specified	Uncertain significance (Aug 14, 2024)
14-21018034-C-T		not specified	Uncertain significance (Jul 14, 2021)
14-21018512-A-G			Benign (Mar 01, 2018)
14-21018786-G-T		not specified	Uncertain significance (Nov 19, 2024)
14-21019117-T-C		not specified	Uncertain significance (May 26, 2022)
14-21019138-G-A		not specified	Uncertain significance (Mar 31, 2024)
14-21019158-C-A		not specified	Uncertain significance (Jan 24, 2024)
14-21019687-T-C		not specified	Uncertain significance (Nov 07, 2022)
14-21019696-A-G		not specified	Uncertain significance (Jul 02, 2024)
14-21019700-T-G		not specified	Uncertain significance (Jun 27, 2022)
14-21019714-A-G		not specified	Uncertain significance (Jan 10, 2023)
14-21019720-T-C		not specified	Uncertain significance (May 06, 2024)
14-21020500-T-C		not specified	Uncertain significance (May 24, 2023)
14-21020798-G-C		not specified	Uncertain significance (Oct 20, 2023)
14-21020837-T-C		not specified	Uncertain significance (Jul 12, 2023)
14-21021833-C-T		not specified	Likely benign (Aug 16, 2021)
14-21021844-A-G		not specified	Uncertain significance (Sep 10, 2024)
14-21022081-C-G		not specified	Uncertain significance (Oct 29, 2024)
14-21022102-C-A		not specified	Uncertain significance (Sep 18, 2023)
14-21022150-C-T		not specified	Uncertain significance (May 10, 2024)
14-21022423-C-A			Benign (May 04, 2018)
14-21022431-G-A		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDRG2	protein_coding	protein_coding	ENST00000556147	15	54110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000220	0.996	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.621	192	218	0.882	0.0000122	2387
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000905
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.0000589	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000589	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Validated targets of C-MYC transcriptional repression (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.743
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.480
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndrg2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; hematopoietic system 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); neoplasm; 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); immune system phenotype

Gene ontology

• Biological process: negative regulation of cytokine production;signal transduction;regulation of vascular endothelial growth factor production;Wnt signaling pathway;substantia nigra development;cell differentiation;negative regulation of smooth muscle cell proliferation;negative regulation of ERK1 and ERK2 cascade;regulation of platelet-derived growth factor production
• Cellular component: nucleus;cytoplasm;Golgi apparatus;cytosol;growth cone;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: molecular_function;protein binding