NUCKS1

nuclear casein kinase and cyclin dependent kinase substrate 1

Basic information

Region (hg38): 1:205712821-205750182

Links

ENSG00000069275 ∙ NCBI:64710 ∙ OMIM:611912 ∙ HGNC:29923 ∙ Uniprot:Q9H1E3 ∙ 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 NUCKS1 gene.

• Inborn genetic diseases (5 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUCKS1 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			5			5
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	6	0	0

Variants in NUCKS1

This is a list of pathogenic ClinVar variants found in the NUCKS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205718341-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-205719642-T-G		not specified	Uncertain significance (Nov 18, 2022)
1-205723953-T-C		not specified	Uncertain significance (Mar 02, 2023)
1-205727734-T-C		not specified	Uncertain significance (Jan 09, 2023)
1-205727805-T-C		not specified	Uncertain significance (Jun 03, 2022)
1-205750014-C-CCGGGGGGGGGGGGGGGGGGGGGGGGG		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUCKS1	protein_coding	protein_coding	ENST00000367142	7	37458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0306	120217	0	1	120218	0.00000416

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	66	134	0.492	0.00000720	1613
Missense in Polyphen		7	26.579	0.26337		298
Synonymous	0.382	47	50.4	0.932	0.00000304	418
Loss of Function	3.37	1	15.2	0.0658	8.77e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000905	0.00000905
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.301
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.901
• hipred: Y
• hipred_score: 0.728
• ghis: 0.700

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nucks1

Gene ontology

• Biological process: double-strand break repair via homologous recombination;cellular glucose homeostasis;regulation of DNA replication;chromatin organization;regulation of transcription by RNA polymerase II;release from viral latency;replication fork processing;gene conversion;interstrand cross-link repair;positive regulation by host of viral transcription;positive regulation by host of viral genome replication;positive regulation of transcription by RNA polymerase II;regulation of insulin receptor signaling pathway;positive regulation of insulin receptor signaling pathway;regulation of DNA strand elongation;cellular response to X-ray;modulation by host of RNA binding by virus;modulation by host of viral RNA-binding transcription factor activity
• Cellular component: chromatin;nuclear chromatin;nucleus;nucleolus;cytoplasm
• Molecular function: DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;double-stranded DNA binding;single-stranded DNA binding;RNA binding;transcription factor binding