NEDD9

neural precursor cell expressed, developmentally down-regulated 9, the group of Cas scaffold proteins

Basic information

Region (hg38): 6:11183298-11382348

Links

ENSG00000111859

∙ NCBI:4739 ∙ OMIM:602265 ∙ HGNC:7733 ∙ Uniprot:Q14511 ∙ 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 NEDD9 gene.

not_specified (109 variants)
not_provided (4 variants)
NEDD9-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEDD9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006403.4. 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				2 clinvar	1 clinvar	3
missense			105 clinvar	5 clinvar		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	105	7	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEDD9	protein_coding	protein_coding	ENST00000379446	7	199051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.126	0.874	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.862	426	479	0.889	0.0000276	5467
Missense in Polyphen		131	166.66	0.78602		1961
Synonymous	1.23	179	201	0.890	0.0000132	1651
Loss of Function	4.18	9	36.1	0.250	0.00000206	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Docking protein which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. May function in transmitting growth control signals between focal adhesions at the cell periphery and the mitotic spindle in response to adhesion or growth factor signals initiating cell proliferation. May play an important role in integrin beta-1 or B cell antigen receptor (BCR) mediated signaling in B- and T-cells. Integrin beta-1 stimulation leads to recruitment of various proteins including CRK, NCK and SHPTP2 to the tyrosine phosphorylated form.;
Pathway: TGF-beta Signaling Pathway;TCR;BCR;EGFR1 (Consensus)

Recessive Scores

pRec: 0.237

Intolerance Scores

loftool: 0.583
rvis_EVS: -0.37
rvis_percentile_EVS: 28.22

Haploinsufficiency Scores

pHI: 0.389
hipred: Y
hipred_score: 0.756
ghis: 0.497

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nedd9
Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; 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); cellular phenotype;

Gene ontology

Biological process: cytoskeleton organization;cell cycle;cell adhesion;signal transduction;integrin-mediated signaling pathway;cell migration;positive regulation of cell migration;regulation of growth;actin filament bundle assembly;cell division;positive regulation of protein tyrosine kinase activity;actin filament reorganization;activation of GTPase activity;positive regulation of substrate adhesion-dependent cell spreading
Cellular component: spindle pole;nucleus;nucleoplasm;cytoplasm;Golgi apparatus;spindle;cytosol;plasma membrane;focal adhesion;cell cortex;lamellipodium
Molecular function: protein binding;protein tyrosine kinase binding