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.

not_specified (38 variants)
not_provided (16 variants)
NDRG4-related_disorder (5 variants)
Hepatoblastoma (1 variants)

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. These statistics are base on transcript: NM_001242835.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar		6
missense			40 clinvar			40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	6	0

Loading clinvar variants...

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