NUDCD1

NudC domain containing 1, the group of NudC family

Basic information

Region (hg38): 8:109240919-109334121

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.

• not_specified (71 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. These statistics are base on transcript: NM_000032869.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			68	3		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	3	0

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