NCL

nucleolin, the group of Small nucleolar RNA protein coding host genes|RNA binding motif containing|DNA helicases|SSU processome

Basic information

Region (hg38): 2:231453531-231483641

Links

ENSG00000115053 ∙ NCBI:4691 ∙ OMIM:164035 ∙ HGNC:7667 ∙ Uniprot:P19338 ∙ 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 NCL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCL 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				4	4	8
missense			20	2	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel				2	1	3
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					2	2
Total	0	0	20	8	9

Variants in NCL

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

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

Position	Type	Phenotype	Significance	ClinVar
2-231455204-G-A		not specified	Uncertain significance (Oct 26, 2024)
2-231455229-C-T		not specified	Uncertain significance (Sep 11, 2024)
2-231455391-C-T			Benign (Aug 24, 2018)
2-231455465-TC-T		Autism	Uncertain significance (-)
2-231455473-C-T		See cases • not specified	Uncertain significance (May 19, 2023)
2-231455506-C-A		not specified	Uncertain significance (Jan 24, 2024)
2-231455570-G-A			Benign (Mar 30, 2018)
2-231455594-C-G		not specified	Uncertain significance (Jul 05, 2023)
2-231456087-T-C			Benign (Jun 10, 2018)
2-231456145-G-GA			Benign (Sep 12, 2018)
2-231456690-T-C		not specified	Uncertain significance (May 09, 2024)
2-231456723-T-G		not specified	Uncertain significance (Aug 12, 2021)
2-231456730-C-T		not specified	Uncertain significance (Oct 25, 2022)
2-231456731-G-A			Benign (Jul 31, 2018)
2-231456744-G-C		not specified	Uncertain significance (Aug 02, 2023)
2-231456767-G-A			Uncertain significance (Sep 01, 2023)
2-231457020-G-T		not specified	Uncertain significance (Jun 24, 2022)
2-231457736-T-C		not specified	Uncertain significance (Aug 28, 2024)
2-231458386-C-T		not specified	Uncertain significance (Feb 28, 2024)
2-231459077-C-T			Likely benign (Jun 23, 2018)
2-231460171-C-T		not specified	Uncertain significance (Jun 24, 2022)
2-231460188-T-C		not specified	Uncertain significance (Dec 22, 2023)
2-231460208-G-A			Likely benign (Feb 01, 2024)
2-231460269-T-C		not specified	Uncertain significance (Oct 02, 2023)
2-231460278-G-A		not specified	Uncertain significance (Nov 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCL	protein_coding	protein_coding	ENST00000322723	14	30111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000788	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.849	333	380	0.877	0.0000201	4691
Missense in Polyphen		28	82.708	0.33854		1142
Synonymous	-1.86	167	139	1.20	0.00000863	1306
Loss of Function	5.22	2	35.6	0.0561	0.00000234	442

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.00219	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000352
Middle Eastern	0.00219	0.00109
South Asian	0.000625	0.000327
Other	0.000327	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. {ECO:0000269|PubMed:10393184}.
• Pathway: Pathogenic Escherichia coli infection - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Pathogenic Escherichia coli infection;VEGFA-VEGFR2 Signaling Pathway;TCR;Aurora B signaling;Validated targets of C-MYC transcriptional activation;Regulation of Telomerase;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.735

Intolerance Scores

• loftool: 0.274
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.27

Haploinsufficiency Scores

• pHI: 0.988
• hipred: Y
• hipred_score: 0.748
• ghis: 0.651

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncl

Zebrafish Information Network

• Gene name: ncl
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: angiogenesis;negative regulation of translation;positive regulation of transcription by RNA polymerase II;cellular response to epidermal growth factor stimulus;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;nucleoplasm;nucleolus;cell cortex;membrane;cytoplasmic ribonucleoprotein granule;extracellular exosome;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding;protein C-terminus binding;telomeric DNA binding;identical protein binding;DNA topoisomerase binding;mRNA 5'-UTR binding