NDRG4

NDRG family member 4, the group of NDRG family

Basic information

Region (hg38): 16:58462846-58513628

Links

ENSG00000103034 ∙ NCBI:65009 ∙ OMIM:614463 ∙ HGNC:14466 ∙ Uniprot:Q9ULP0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• achromatopsia (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDRG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDRG4 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	3	4
missense			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4		4
non coding				17	28	45
Total	0	0	32	18	31

Variants in NDRG4

This is a list of pathogenic ClinVar variants found in the NDRG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58463936-C-T			Likely benign (Dec 22, 2021)
16-58463938-C-T			Likely benign (May 25, 2019)
16-58464080-G-T			Likely benign (Apr 16, 2019)
16-58464475-C-A			Likely benign (Jan 15, 2022)
16-58487518-TA-T			Likely benign (Nov 22, 2019)
16-58487526-A-G			Benign (Aug 21, 2019)
16-58487860-A-G			Likely benign (Nov 29, 2019)
16-58494768-G-A			Likely benign (Nov 29, 2019)
16-58494832-T-TA			Benign (Oct 22, 2019)
16-58494832-T-TAA			Benign (Aug 21, 2019)
16-58494832-T-TAAA			Likely benign (Feb 13, 2020)
16-58494908-G-A			Benign (Jan 10, 2019)
16-58494972-C-T		NDRG4-related disorder	Likely benign (Sep 18, 2019)
16-58495135-G-A			Likely benign (Jun 12, 2019)
16-58499805-G-T			Benign (Apr 09, 2019)
16-58500028-A-C			Benign (Jan 10, 2019)
16-58500126-A-G			Likely benign (Mar 20, 2019)
16-58503518-G-A			Likely benign (Jun 12, 2019)
16-58503806-C-G		not specified	Uncertain significance (Apr 29, 2024)
16-58503809-C-G		not specified	Uncertain significance (Jan 07, 2022)
16-58503823-G-A		not specified	Uncertain significance (Aug 05, 2024)
16-58503843-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-58503844-G-A		not specified	Uncertain significance (Jan 17, 2024)
16-58503852-C-T		not specified	Uncertain significance (Sep 27, 2022)
16-58503993-G-A			Benign (Jan 10, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDRG4	protein_coding	protein_coding	ENST00000394282	16	50783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0116	0.988	125727	0	18	125745	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.572	207	232	0.894	0.0000140	2547
Missense in Polyphen		75	81.063	0.92521		872
Synonymous	-0.0884	98	96.9	1.01	0.00000637	777
Loss of Function	3.14	8	24.9	0.321	0.00000117	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.0000976	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the maintenance of intracerebral BDNF levels within the normal range, which is necessary for the preservation of spatial learning and the resistance to neuronal cell death caused by ischemic stress (By similarity). May enhance growth factor-induced ERK1 and ERK2 phosphorylation, including that induced by PDGF and FGF. May attenuate NGF-promoted ELK1 phosphorylation in a microtubule-dependent manner. {ECO:0000250, ECO:0000269|PubMed:12755708}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.787
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.88

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.604
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndrg4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); growth/size/body region phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: ndrg4
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: heart looping;signal transduction;brain development;visual learning;negative regulation of platelet-derived growth factor receptor signaling pathway;positive regulation of neuron projection development;negative regulation of smooth muscle cell migration;cell differentiation;embryonic heart tube development;vesicle docking;negative regulation of smooth muscle cell proliferation;cardiac muscle cell proliferation;cell migration involved in heart development;positive regulation of ERK1 and ERK2 cascade;regulation of endocytic recycling
• Cellular component: cytoplasm;mitochondrion;endoplasmic reticulum membrane;cytosol;basolateral plasma membrane;cell projection membrane
• Molecular function: molecular_function;protein binding