NOLC1

nucleolar and coiled-body phosphoprotein 1

Basic information

Region (hg38): 10:102152176-102163871

Links

ENSG00000166197 ∙ NCBI:9221 ∙ OMIM:602394 ∙ HGNC:15608 ∙ Uniprot:Q14978 ∙ 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 NOLC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOLC1 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				3	3	6
missense			65	7	2	74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	65	12	5

Variants in NOLC1

This is a list of pathogenic ClinVar variants found in the NOLC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-102152426-A-T		not specified	Uncertain significance (May 29, 2024)
10-102152430-G-T		not specified	Uncertain significance (Apr 09, 2024)
10-102152433-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-102152441-C-G		not specified	Uncertain significance (Mar 02, 2023)
10-102152452-G-A			Benign (Dec 31, 2019)
10-102157035-A-G		not specified	Uncertain significance (Feb 06, 2023)
10-102157062-G-C		not specified	Uncertain significance (Nov 07, 2022)
10-102157245-C-G		not specified	Uncertain significance (Feb 05, 2024)
10-102157257-C-G		not specified	Uncertain significance (Aug 12, 2021)
10-102157262-T-A		not specified	Uncertain significance (Jun 13, 2023)
10-102157283-A-C		not specified	Uncertain significance (Dec 10, 2024)
10-102157451-G-A		not specified	Likely benign (Aug 19, 2023)
10-102157452-G-A		not specified	Uncertain significance (Feb 01, 2023)
10-102157460-C-T		not specified	Uncertain significance (Mar 20, 2024)
10-102157490-A-T		not specified	Uncertain significance (Mar 31, 2024)
10-102157514-G-A		not specified	Uncertain significance (Sep 01, 2024)
10-102157515-A-G		not specified	Uncertain significance (Jan 10, 2023)
10-102157529-G-C		not specified	Uncertain significance (Nov 14, 2023)
10-102158077-C-T		not specified	Likely benign (Dec 01, 2022)
10-102158168-A-G		not specified	Uncertain significance (Mar 07, 2024)
10-102158172-C-A		not specified	Uncertain significance (Dec 20, 2023)
10-102158172-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-102159199-C-G		not specified	Uncertain significance (Jan 08, 2024)
10-102159242-T-C			Likely benign (Dec 01, 2022)
10-102159440-C-G		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOLC1	protein_coding	protein_coding	ENST00000605788	13	11695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000104	1.00	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.00	427	373	1.15	0.0000182	4563
Missense in Polyphen		30	33.875	0.8856		407
Synonymous	-0.860	151	138	1.09	0.00000700	1344
Loss of Function	3.38	13	34.4	0.378	0.00000204	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000231	0.000139
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.0000981	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleolar protein that acts as a regulator of RNA polymerase I by connecting RNA polymerase I with enzymes responsible for ribosomal processing and modification (PubMed:10567578, PubMed:26399832). Required for neural crest specification: following monoubiquitination by the BCR(KBTBD8) complex, associates with TCOF1 and acts as a platform to connect RNA polymerase I with enzymes responsible for ribosomal processing and modification, leading to remodel the translational program of differentiating cells in favor of neural crest specification (PubMed:26399832). Involved in nucleologenesis, possibly by playing a role in the maintenance of the fundamental structure of the fibrillar center and dense fibrillar component in the nucleolus (PubMed:9016786). It has intrinsic GTPase and ATPase activities (PubMed:9016786). {ECO:0000269|PubMed:10567578, ECO:0000269|PubMed:26399832, ECO:0000269|PubMed:9016786}.
• Pathway: integrin signaling pathway (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.750
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.622
• hipred: Y
• hipred_score: 0.573
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nolc1

Zebrafish Information Network

• Gene name: nolc1
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: mitotic cell cycle;rRNA processing;regulation of translation;response to osmotic stress;nucleolus organization;positive regulation of cell population proliferation;neural crest formation;neural crest cell development;box H/ACA snoRNA metabolic process;regulation of protein import into nucleus;positive regulation of transcription, DNA-templated
• Cellular component: fibrillar center;nucleoplasm;nucleolus;cytoplasm;Cajal body;box C/D snoRNP complex;box H/ACA snoRNP complex
• Molecular function: RNA polymerase I core binding;DNA binding;DNA-binding transcription factor activity;RNA binding;protein binding;ATP binding;GTP binding;transcription factor binding;nuclear localization sequence binding;protein domain specific binding;box C/D snoRNA binding;box H/ACA snoRNA binding;protein heterodimerization activity;box C/D snoRNP complex binding;box H/ACA snoRNP complex binding