NUDCD1

NudC domain containing 1, the group of NudC family

Basic information

Region (hg38): 8:109240918-109334121

Links

ENSG00000120526 ∙ NCBI:84955 ∙ OMIM:606109 ∙ HGNC:24306 ∙ Uniprot:Q96RS6 ∙ 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 NUDCD1 gene.

• Inborn genetic diseases (31 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDCD1 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in NUDCD1

This is a list of pathogenic ClinVar variants found in the NUDCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-109243028-T-C		not specified	Uncertain significance (Dec 02, 2022)
8-109243179-T-C		not specified	Uncertain significance (Dec 06, 2022)
8-109243185-T-G		not specified	Uncertain significance (Aug 12, 2021)
8-109243251-T-G		not specified	Uncertain significance (Aug 08, 2023)
8-109243284-T-C		not specified	Uncertain significance (Oct 04, 2022)
8-109245405-T-A		not specified	Uncertain significance (May 23, 2023)
8-109245444-A-G		not specified	Uncertain significance (May 23, 2023)
8-109245472-C-T		not specified	Uncertain significance (Dec 13, 2021)
8-109271045-A-G		not specified	Uncertain significance (Jan 23, 2024)
8-109271102-G-C		not specified	Uncertain significance (Sep 01, 2021)
8-109275381-G-T		not specified	Uncertain significance (Aug 07, 2023)
8-109275423-C-T		not specified	Uncertain significance (Oct 26, 2022)
8-109280976-C-G		not specified	Uncertain significance (Oct 30, 2023)
8-109280995-C-G		not specified	Uncertain significance (Jul 08, 2022)
8-109281004-T-C		not specified	Uncertain significance (Nov 08, 2022)
8-109281013-G-A		not specified	Uncertain significance (Nov 06, 2023)
8-109281016-G-A		not specified	Uncertain significance (Dec 22, 2023)
8-109281058-A-G		not specified	Uncertain significance (Feb 03, 2022)
8-109281080-A-T		not specified	Uncertain significance (Aug 23, 2021)
8-109281140-C-A		not specified	Uncertain significance (Jan 03, 2024)
8-109281169-G-A		not specified	Uncertain significance (Nov 13, 2023)
8-109289848-A-T		not specified	Uncertain significance (Oct 06, 2021)
8-109289850-T-C		not specified	Uncertain significance (Jul 12, 2023)
8-109289895-G-A		not specified	Likely benign (Jun 16, 2023)
8-109289901-T-C		not specified	Likely benign (Jun 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDCD1	protein_coding	protein_coding	ENST00000239690	10	93467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.67e-11	0.688	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.502	279	304	0.919	0.0000151	3830
Missense in Polyphen		70	70.187	0.99734		863
Synonymous	0.385	97	102	0.951	0.00000466	1069
Loss of Function	1.53	21	30.1	0.699	0.00000163	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000368
Ashkenazi Jewish	0.000466	0.000397
East Asian	0.000232	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000234	0.000229
Middle Eastern	0.000232	0.000217
South Asian	0.000710	0.000653
Other	0.000180	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0836

Intolerance Scores

• loftool: 0.975
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.06

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.289
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudcd1

Gene ontology

• Biological process: immune system process
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding