NUDCD3

NudC domain containing 3, the group of NudC family

Basic information

Region (hg38): 7:44379119-44490658

Links

ENSG00000015676 ∙ NCBI:23386 ∙ OMIM:610296 ∙ HGNC:22208 ∙ Uniprot:Q8IVD9 ∙ 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 NUDCD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDCD3 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in NUDCD3

This is a list of pathogenic ClinVar variants found in the NUDCD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-44386027-C-T		not specified	Uncertain significance (Nov 25, 2024)
7-44386060-C-T		not specified	Uncertain significance (Nov 20, 2024)
7-44386067-C-T		not specified	Uncertain significance (Mar 16, 2024)
7-44392313-G-A		not specified	Uncertain significance (Aug 11, 2024)
7-44392334-T-G			Likely pathogenic (Dec 18, 2024)
7-44392362-C-T		not specified	Uncertain significance (Dec 02, 2022)
7-44392365-C-T		not specified	Uncertain significance (May 15, 2024)
7-44392392-T-C		not specified	Uncertain significance (Aug 03, 2022)
7-44404445-C-T		not specified	Uncertain significance (Feb 06, 2023)
7-44404513-A-G		not specified	Uncertain significance (Jun 10, 2024)
7-44404520-C-T		not specified	Uncertain significance (Jul 21, 2022)
7-44404522-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-44404532-T-C		not specified	Uncertain significance (Dec 02, 2024)
7-44485075-C-G		not specified	Uncertain significance (Jul 20, 2022)
7-44485139-A-C		not specified	Uncertain significance (Oct 27, 2023)
7-44485169-G-A		not specified	Uncertain significance (Apr 22, 2024)
7-44485170-C-T		not specified	Uncertain significance (Dec 15, 2023)
7-44485197-C-T		not specified	Uncertain significance (Oct 07, 2024)
7-44485200-C-T		not specified	Uncertain significance (May 26, 2024)
7-44485257-G-A		not specified	Uncertain significance (Oct 07, 2024)
7-44490467-C-T		not specified	Uncertain significance (Feb 28, 2023)
7-44490479-T-C		not specified	Uncertain significance (Jul 20, 2022)
7-44490584-G-A		not specified	Uncertain significance (Apr 23, 2024)
7-44490588-C-A		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDCD3	protein_coding	protein_coding	ENST00000355451	6	111760

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.448	0.552	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.851	172	206	0.833	0.0000108	2363
Missense in Polyphen		35	54.221	0.6455		633
Synonymous	-0.235	84	81.3	1.03	0.00000455	681
Loss of Function	3.14	4	18.6	0.215	0.00000105	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000563	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000563	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.369
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.166
• hipred: Y
• hipred_score: 0.581
• ghis: 0.554

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudcd3

Gene ontology

• Biological process: protein folding;developmental process;cilium assembly;protein localization to pericentriolar material
• Cellular component: cytoplasm;cytoplasmic dynein complex
• Molecular function: protein binding;unfolded protein binding