NEDD9

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

Basic information

Region (hg38): 6:11183297-11382348

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.

• Inborn genetic diseases (34 variants)
• not provided (4 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.

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				2	1	3
missense			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	1

Variants in NEDD9

This is a list of pathogenic ClinVar variants found in the NEDD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-11185191-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-11185271-A-C		not specified	Uncertain significance (Jun 24, 2022)
6-11185299-T-C		not specified	Uncertain significance (May 31, 2023)
6-11185349-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-11185430-C-A		not specified	Uncertain significance (Mar 07, 2023)
6-11185446-T-G		not specified	Uncertain significance (May 17, 2023)
6-11185490-A-G		not specified	Uncertain significance (Nov 17, 2022)
6-11185515-G-A		not specified	Uncertain significance (Jan 11, 2023)
6-11185553-C-A		not specified	Uncertain significance (Oct 26, 2022)
6-11185581-T-G		not specified	Uncertain significance (Apr 11, 2023)
6-11185587-G-A		not specified	Uncertain significance (Sep 23, 2023)
6-11185629-C-T		not specified	Uncertain significance (Mar 20, 2023)
6-11185630-G-A			Likely benign (May 01, 2022)
6-11188225-T-C		not specified	Uncertain significance (Oct 26, 2021)
6-11188299-C-G		not specified	Uncertain significance (Dec 21, 2022)
6-11189970-G-A			Benign/Likely benign (Oct 01, 2023)
6-11189975-C-T		not specified	Uncertain significance (Jan 02, 2024)
6-11190032-G-A		not specified	Uncertain significance (Oct 22, 2021)
6-11190126-G-A			Benign (Apr 12, 2018)
6-11190175-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-11190281-G-C		not specified	Uncertain significance (Dec 07, 2023)
6-11190358-T-C		NEDD9-related disorder	Likely benign (Feb 10, 2022)
6-11190385-G-T		not specified	Uncertain significance (Mar 01, 2024)
6-11190559-C-T		not specified	Uncertain significance (Oct 12, 2022)
6-11190590-G-T		not specified	Uncertain significance (Sep 28, 2022)

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