NEDD8-MDP1

NEDD8-MDP1 readthrough

Basic information

Region (hg38): 14:24213954-24232352

Links

ENSG00000255526 ∙ NCBI:100528064 ∙ ∙ HGNC:39551 ∙ ∙ ∙ 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 NEDD8-MDP1 gene.

• Malignant tumor of prostate (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEDD8-MDP1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	2	0	0

Variants in NEDD8-MDP1

This is a list of pathogenic ClinVar variants found in the NEDD8-MDP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24214070-G-C		not specified	Uncertain significance (Mar 19, 2024)
14-24214076-G-A		not specified	Uncertain significance (Nov 09, 2021)
14-24214099-T-C		not specified	Likely benign (Dec 11, 2023)
14-24214105-T-G		not specified	Likely benign (May 14, 2024)
14-24214109-G-A		not specified	Uncertain significance (Apr 27, 2022)
14-24214124-C-T		not specified	Uncertain significance (Feb 09, 2023)
14-24214135-G-A		not specified	Likely benign (Dec 28, 2023)
14-24214313-G-C		Malignant tumor of prostate	Uncertain significance (-)
14-24214314-T-A		not specified	Uncertain significance (Jul 19, 2022)
14-24214336-C-T		not specified	Uncertain significance (Dec 15, 2022)
14-24214337-G-A		not specified	Uncertain significance (Jun 28, 2023)
14-24214577-T-C		not specified	Uncertain significance (Jan 31, 2024)
14-24215571-G-A		not specified	Uncertain significance (Oct 21, 2021)
14-24215628-C-A		not specified	Uncertain significance (Jul 08, 2022)
14-24215636-C-T		not specified	Uncertain significance (Jun 22, 2023)
14-24215924-T-C		not specified	Uncertain significance (Dec 07, 2021)
14-24215951-G-C		not specified	Uncertain significance (Jun 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEDD8-MDP1	protein_coding	protein_coding	ENST00000534348	7	18398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00250	0.937	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.887	69	93.1	0.741	0.00000496	1114
Missense in Polyphen		21	37.979	0.55294		457
Synonymous	-0.142	34	33.0	1.03	0.00000166	316
Loss of Function	1.64	6	12.2	0.493	6.39e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000296	0.000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Biological process: dephosphorylation
• Molecular function: phosphatase activity