NEDD1

NEDD1 gamma-tubulin ring complex targeting factor, the group of WD repeat domain containing

Basic information

Region (hg38): 12:96907224-96953780

Links

ENSG00000139350 ∙ NCBI:121441 ∙ OMIM:600372 ∙ HGNC:7723 ∙ Uniprot:Q8NHV4 ∙ 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 NEDD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEDD1 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			42	3		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	42	3	0

Variants in NEDD1

This is a list of pathogenic ClinVar variants found in the NEDD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-96909754-G-A		not specified	Uncertain significance (Feb 16, 2023)
12-96909839-A-G		not specified	Uncertain significance (Jun 18, 2024)
12-96909893-A-G		not specified	Uncertain significance (Aug 01, 2024)
12-96912723-A-G		not specified	Uncertain significance (Jan 18, 2025)
12-96912791-G-C		not specified	Uncertain significance (Nov 14, 2024)
12-96917651-A-T		not specified	Uncertain significance (Nov 10, 2022)
12-96917655-C-G		not specified	Uncertain significance (Nov 07, 2023)
12-96920013-C-T		not specified	Uncertain significance (Aug 30, 2022)
12-96920036-A-G		not specified	Likely benign (Aug 03, 2022)
12-96920072-C-T		not specified	Uncertain significance (Apr 25, 2023)
12-96920117-A-G		not specified	Uncertain significance (Apr 26, 2023)
12-96934977-C-T		not specified	Uncertain significance (Nov 22, 2022)
12-96934985-C-A		not specified	Uncertain significance (Aug 08, 2022)
12-96934986-A-C		not specified	Uncertain significance (Aug 08, 2022)
12-96934998-C-G		not specified	Uncertain significance (Jun 22, 2021)
12-96935063-A-G		not specified	Uncertain significance (Aug 30, 2022)
12-96935093-A-G		not specified	Uncertain significance (Jul 26, 2022)
12-96935112-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-96935171-A-C		not specified	Uncertain significance (May 21, 2024)
12-96936631-C-G		not specified	Uncertain significance (Feb 19, 2025)
12-96936660-A-G		not specified	Uncertain significance (Sep 22, 2023)
12-96936696-C-T		not specified	Uncertain significance (Apr 18, 2023)
12-96936722-A-C		not specified	Uncertain significance (Jun 22, 2021)
12-96936746-G-C		not specified	Uncertain significance (May 05, 2023)
12-96937294-A-T		not specified	Uncertain significance (Dec 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEDD1	protein_coding	protein_coding	ENST00000557644	15	46129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.422	0.578	125716	0	26	125742	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	329	346	0.950	0.0000169	4376
Missense in Polyphen		93	116.44	0.79866		1504
Synonymous	0.647	111	120	0.925	0.00000608	1260
Loss of Function	4.05	7	31.6	0.222	0.00000149	433

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000186
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000804	0.0000791
Middle Eastern	0.000163	0.000163
South Asian	0.0000983	0.0000980
Other	0.000376	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for mitosis progression. Promotes the nucleation of microtubules from the spindle. {ECO:0000269|PubMed:19029337, ECO:0000269|PubMed:19509060}.
• Pathway: Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.814
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.221
• hipred: Y
• hipred_score: 0.653
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.576

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nedd1

Zebrafish Information Network

• Gene name: nedd1
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;regulation of G2/M transition of mitotic cell cycle;cell division;protein localization to centrosome;ciliary basal body-plasma membrane docking
• Cellular component: pericentriolar material;spindle pole;centrosome;centriole;cytosol;ciliary basal body;apical part of cell
• Molecular function: protein binding