GNL3

G protein nucleolar 3, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 3:52681156-52694497

Links

ENSG00000163938 ∙ NCBI:26354 ∙ OMIM:608011 ∙ HGNC:29931 ∙ Uniprot:Q9BVP2 ∙ 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 GNL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNL3 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			22	3		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	0

Variants in GNL3

This is a list of pathogenic ClinVar variants found in the GNL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52686103-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-52686808-G-A		not specified	Uncertain significance (Apr 01, 2024)
3-52687349-C-T		not specified	Uncertain significance (Jan 27, 2022)
3-52687533-A-G		not specified	Uncertain significance (Jun 13, 2024)
3-52687551-A-G		not specified	Likely benign (Jun 16, 2024)
3-52688146-C-T		not specified	Uncertain significance (Jul 11, 2023)
3-52689168-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-52689192-T-A		not specified	Uncertain significance (Feb 16, 2023)
3-52690946-G-A		not specified	Likely benign (Jun 21, 2023)
3-52690967-C-T		not specified	Uncertain significance (Nov 18, 2022)
3-52690972-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-52690984-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-52691017-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-52691557-G-A		not specified	Uncertain significance (Jun 07, 2023)
3-52692931-T-A		not specified	Uncertain significance (Nov 09, 2021)
3-52692933-G-A		not specified	Uncertain significance (Aug 11, 2023)
3-52693000-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-52693020-A-C		not specified	Uncertain significance (Jul 25, 2023)
3-52693241-G-C		not specified	Likely benign (Jun 12, 2023)
3-52693436-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-52693488-T-A		not specified	Uncertain significance (Jan 27, 2022)
3-52693510-A-C		not specified	Uncertain significance (Mar 16, 2022)
3-52693679-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-52693805-G-A		not specified	Uncertain significance (Jul 05, 2023)
3-52694042-C-G		not specified	Likely benign (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNL3	protein_coding	protein_coding	ENST00000418458	15	13337

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.99e-19	0.00655	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.283	272	285	0.953	0.0000137	3628
Missense in Polyphen		61	87.494	0.69719		1186
Synonymous	-1.50	118	99.1	1.19	0.00000484	985
Loss of Function	0.349	30	32.1	0.934	0.00000164	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000362	0.000360
Middle Eastern	0.000381	0.000381
South Asian	0.000299	0.000294
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required to maintain the proliferative capacity of stem cells. Stabilizes MDM2 by preventing its ubiquitination, and hence proteasomal degradation (By similarity). {ECO:0000250, ECO:0000269|PubMed:12464630, ECO:0000269|PubMed:16012751}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.59

Haploinsufficiency Scores

• pHI: 0.945
• hipred: N
• hipred_score: 0.428
• ghis: 0.512

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnl3
• Phenotype: embryo phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: gnl3
• Affected structure: radial glial cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: cell population proliferation;stem cell division;stem cell population maintenance;positive regulation of telomere maintenance;positive regulation of protein sumoylation;regulation of cell population proliferation;positive regulation of pri-miRNA transcription by RNA polymerase II;positive regulation of protein localization to chromosome, telomeric region
• Cellular component: extracellular space;nucleus;nucleolus;membrane;nuclear body
• Molecular function: RNA binding;protein binding;GTP binding;mRNA 5'-UTR binding