GNL3L

G protein nucleolar 3 like

Basic information

Region (hg38): X:54530183-54621521

Links

ENSG00000130119 ∙ NCBI:54552 ∙ OMIM:300873 ∙ HGNC:25553 ∙ Uniprot:Q9NVN8 ∙ 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 GNL3L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNL3L 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				2		2
missense			42	7		49
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	9	1

Variants in GNL3L

This is a list of pathogenic ClinVar variants found in the GNL3L region.

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

Position	Type	Phenotype	Significance	ClinVar
X-54539057-G-A		not specified	Likely benign (Dec 17, 2021)
X-54539061-G-A		not specified	Uncertain significance (Jul 27, 2021)
X-54539064-C-A		not specified	Uncertain significance (Dec 17, 2021)
X-54540175-C-T			Likely benign (Apr 01, 2022)
X-54540206-T-G		not specified	Uncertain significance (May 02, 2024)
X-54540225-G-C		not specified	Uncertain significance (Jun 02, 2023)
X-54540229-TAAA-T			Benign (Dec 20, 2017)
X-54541279-G-A		not specified	Uncertain significance (Mar 29, 2022)
X-54541336-A-G		not specified	Uncertain significance (Jan 20, 2023)
X-54541342-A-G		not specified	Uncertain significance (Dec 25, 2024)
X-54541366-C-T			Likely benign (Nov 01, 2024)
X-54542977-A-C		not specified	Uncertain significance (Mar 03, 2025)
X-54542999-C-T			Likely benign (Apr 01, 2023)
X-54543000-G-A		not specified	Uncertain significance (Mar 20, 2023)
X-54543228-A-G		not specified	Uncertain significance (Jul 20, 2022)
X-54543297-C-G		not specified	Uncertain significance (Sep 12, 2023)
X-54543313-A-G		not specified	Uncertain significance (Nov 08, 2024)
X-54544234-A-G		not specified	Uncertain significance (Feb 02, 2023)
X-54544240-G-A		not specified	Uncertain significance (Sep 20, 2023)
X-54544277-T-C		not specified	Uncertain significance (Jan 09, 2025)
X-54548233-G-A		not specified	Uncertain significance (Dec 08, 2023)
X-54548236-G-C		not specified	Uncertain significance (Aug 19, 2024)
X-54548331-C-T		not specified	Uncertain significance (Aug 08, 2022)
X-54548344-T-C		not specified	Uncertain significance (Nov 18, 2023)
X-54550972-A-G		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNL3L	protein_coding	protein_coding	ENST00000336470	15	30861

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00442	121086	1	0	121087	0.00000413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	188	248	0.757	0.0000209	3847
Missense in Polyphen		50	89.865	0.55639		1503
Synonymous	0.118	89	90.4	0.984	0.00000739	1093
Loss of Function	3.98	1	20.4	0.0489	0.00000142	380

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000556	0.0000351
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stabilizes TERF1 telomeric association by preventing TERF1 recruitment by PML. Stabilizes TERF1 protein by preventing its ubiquitination and hence proteasomal degradation. Does so by interfering with TERF1-binding to FBXO4 E3 ubiquitin-protein ligase. Required for cell proliferation. By stabilizing TRF1 protein during mitosis, promotes metaphase-to-anaphase transition. Stabilizes MDM2 protein by preventing its ubiquitination, and hence proteasomal degradation. By acting on MDM2, may affect TP53 activity. Required for normal processing of ribosomal pre-rRNA. Binds GTP. {ECO:0000269|PubMed:16251348, ECO:0000269|PubMed:17034816, ECO:0000269|PubMed:19487455, ECO:0000269|PubMed:21132010}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.123
• hipred: Y
• hipred_score: 0.704
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.259

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnl3l

Zebrafish Information Network

• Gene name: gnl3l
• Affected structure: posterior chamber swim bladder
• Phenotype tag: abnormal
• Phenotype quality: uninflated

Gene ontology

• Biological process: negative regulation of protein ubiquitination;regulation of protein stability;negative regulation of protein binding;negative regulation of telomere maintenance via telomerase;negative regulation of protein sumoylation;ribosome biogenesis;positive regulation of protein homodimerization activity;positive regulation of protein localization to chromosome, telomeric region
• Cellular component: nucleus;telomerase holoenzyme complex;nucleolus;cytosol;membrane
• Molecular function: RNA binding;protein binding;GTP binding