NDRG3

NDRG family member 3, the group of NDRG family

Basic information

Region (hg38): 20:36651766-36746090

Links

ENSG00000101079 ∙ NCBI:57446 ∙ OMIM:605273 ∙ HGNC:14462 ∙ Uniprot:Q9UGV2 ∙ 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 NDRG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDRG3 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in NDRG3

This is a list of pathogenic ClinVar variants found in the NDRG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36653563-G-C		not specified	Uncertain significance (Dec 20, 2023)
20-36653608-A-G		not specified	Uncertain significance (Nov 12, 2021)
20-36653614-C-T		not specified	Uncertain significance (Feb 17, 2023)
20-36653660-G-A		not specified	Uncertain significance (Jul 12, 2023)
20-36653671-C-T		not specified	Uncertain significance (Mar 20, 2024)
20-36656388-G-C		not specified	Uncertain significance (Feb 25, 2025)
20-36656520-C-G		not specified	Uncertain significance (Nov 07, 2023)
20-36656525-T-G		not specified	Uncertain significance (Dec 12, 2023)
20-36660368-C-T		not specified	Uncertain significance (Sep 12, 2023)
20-36660374-T-C		not specified	Uncertain significance (Aug 17, 2022)
20-36665065-G-A		not specified	Uncertain significance (Jan 20, 2023)
20-36665272-A-G		not specified	Uncertain significance (Sep 17, 2021)
20-36665299-C-T		not specified	Uncertain significance (Dec 02, 2024)
20-36666386-A-C		not specified	Uncertain significance (May 13, 2024)
20-36671357-G-A		not specified	Uncertain significance (Aug 10, 2024)
20-36671394-A-G		not specified	Uncertain significance (May 06, 2024)
20-36687498-G-A		not specified	Uncertain significance (Dec 20, 2023)
20-36687529-G-A		not specified	Uncertain significance (Sep 24, 2024)
20-36687532-C-T		not specified	Uncertain significance (Nov 07, 2024)
20-36687578-C-G		not specified	Uncertain significance (May 08, 2024)
20-36687588-A-C		not specified	Uncertain significance (Dec 19, 2023)
20-36687594-G-T		not specified	Uncertain significance (Dec 17, 2024)
20-36688726-T-C		not specified	Uncertain significance (Mar 24, 2023)
20-36688745-T-C		not specified	Uncertain significance (Aug 10, 2021)
20-36688748-C-T		not specified	Uncertain significance (Jul 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDRG3	protein_coding	protein_coding	ENST00000349004	15	94313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.366	0.634	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	161	207	0.777	0.0000105	2465
Missense in Polyphen		56	74.438	0.7523		923
Synonymous	1.75	57	76.4	0.746	0.00000401	710
Loss of Function	3.69	6	26.5	0.226	0.00000141	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000983	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0769

Intolerance Scores

• loftool: 0.588
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.547
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.623

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndrg3
• 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)

Zebrafish Information Network

• Gene name: ndrg3a
• Affected structure: developmental growth
• Phenotype tag: abnormal
• Phenotype quality: delayed

Gene ontology

• Biological process: signal transduction;spermatogenesis;cell differentiation;negative regulation of cell growth
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: molecular_function