NUDCD2

NudC domain containing 2, the group of NudC family

Basic information

Region (hg38): 5:163446526-163460404

Links

ENSG00000170584 ∙ NCBI:134492 ∙ OMIM:620136 ∙ HGNC:30535 ∙ Uniprot:Q8WVJ2 ∙ 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 NUDCD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDCD2 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in NUDCD2

This is a list of pathogenic ClinVar variants found in the NUDCD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-163453974-T-G		not specified	Uncertain significance (Apr 24, 2023)
5-163454005-T-C		not specified	Uncertain significance (Feb 28, 2024)
5-163456951-G-A		not specified	Uncertain significance (Mar 14, 2025)
5-163457009-G-C		not specified	Uncertain significance (May 28, 2024)
5-163457067-C-T		not specified	Uncertain significance (Mar 25, 2024)
5-163457604-G-C		not specified	Uncertain significance (Jan 04, 2025)
5-163459867-G-A		not specified	Uncertain significance (Nov 27, 2023)
5-163459902-C-T		not specified	Uncertain significance (May 03, 2023)
5-163459903-G-C		not specified	Uncertain significance (Feb 02, 2024)
5-163459912-G-A		not specified	Uncertain significance (Jan 30, 2024)
5-163459944-G-A		not specified	Uncertain significance (Mar 20, 2024)
5-163459954-G-T		not specified	Uncertain significance (Jun 30, 2024)
5-163460010-C-A		not specified	Uncertain significance (Jan 30, 2025)
5-163460020-C-T		not specified	Uncertain significance (Apr 25, 2023)
5-163460022-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDCD2	protein_coding	protein_coding	ENST00000302764	4	13615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00320	0.837	125698	0	46	125744	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.181	79	83.7	0.944	0.00000388	1011
Missense in Polyphen		16	26.444	0.60504		341
Synonymous	-0.728	37	31.8	1.16	0.00000150	302
Loss of Function	1.17	5	8.71	0.574	3.73e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000464	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000545	0.000544
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000545	0.000544
South Asian	0.0000659	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the LIS1/dynein pathway by stabilizing LIS1 with Hsp90 chaperone. {ECO:0000269|PubMed:20133715}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.721
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.315
• hipred: N
• hipred_score: 0.418
• ghis: 0.698

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudcd2

Gene ontology

• Biological process: protein folding;developmental process
• Cellular component: condensed chromosome kinetochore;spindle pole;cytoplasm;microtubule organizing center
• Molecular function: protein binding;unfolded protein binding