GNL2

G protein nucleolar 2

Basic information

Region (hg38): 1:37566816-37595937

Links

ENSG00000134697 ∙ NCBI:29889 ∙ OMIM:609365 ∙ HGNC:29925 ∙ Uniprot:Q13823 ∙ 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 GNL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNL2 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			65	3		68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	65	3	0

Variants in GNL2

This is a list of pathogenic ClinVar variants found in the GNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37566881-G-A		not specified	Uncertain significance (Jul 16, 2021)
1-37566913-T-G		not specified	Uncertain significance (Jul 12, 2022)
1-37566916-T-G		not specified	Uncertain significance (Aug 30, 2022)
1-37566941-C-G		not specified	Uncertain significance (Mar 31, 2023)
1-37566955-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-37566961-C-T		not specified	Uncertain significance (Nov 03, 2022)
1-37566962-G-A		not specified	Uncertain significance (Jun 03, 2024)
1-37566974-T-C		not specified	Uncertain significance (Sep 26, 2024)
1-37566982-C-T		not specified	Likely benign (Jul 17, 2023)
1-37566983-G-A		not specified	Uncertain significance (Nov 15, 2023)
1-37567000-C-T		not specified	Uncertain significance (Oct 08, 2024)
1-37567707-G-A		not specified	Uncertain significance (Jan 21, 2025)
1-37568332-T-A		not specified	Uncertain significance (Apr 04, 2024)
1-37568905-G-C		not specified	Uncertain significance (Jul 30, 2024)
1-37568908-A-G		not specified	Uncertain significance (Feb 22, 2025)
1-37568927-T-C		not specified	Uncertain significance (Apr 12, 2022)
1-37568947-T-C		not specified	Uncertain significance (Dec 11, 2024)
1-37568974-G-A		not specified	Uncertain significance (Dec 28, 2024)
1-37568987-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-37568989-G-A		not specified	Likely benign (Jan 09, 2024)
1-37568993-C-T		not specified	Uncertain significance (Feb 25, 2025)
1-37569020-C-T		not specified	Uncertain significance (Nov 08, 2024)
1-37569025-T-C		not specified	Uncertain significance (Nov 14, 2024)
1-37569149-G-C		not specified	Uncertain significance (Apr 27, 2024)
1-37569155-T-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNL2	protein_coding	protein_coding	ENST00000373062	16	29120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000652	1.00	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.276	394	410	0.962	0.0000230	4811
Missense in Polyphen		122	146.31	0.83385		1694
Synonymous	-0.0909	139	138	1.01	0.00000722	1358
Loss of Function	3.85	15	41.9	0.358	0.00000239	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.000330	0.000326
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000250	0.000246
Middle Eastern	0.000330	0.000326
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase that associates with pre-60S ribosomal subunits in the nucleolus and is required for their nuclear export and maturation (By similarity). May promote cell proliferation possibly by increasing p53/TP53 protein levels, and consequently those of its downstream product CDKN1A/p21, and decreasing RPL23A protein levels (PubMed:26203195). {ECO:0000250, ECO:0000269|PubMed:26203195}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.771
• rvis_EVS: -1
• rvis_percentile_EVS: 8.54

Haploinsufficiency Scores

• pHI: 0.900
• hipred: Y
• hipred_score: 0.758
• ghis: 0.627

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0619

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnl2

Zebrafish Information Network

• Gene name: gnl2
• Affected structure: Muller cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: biological_process;ribosome biogenesis
• Cellular component: nucleus;nucleolus;membrane
• Molecular function: RNA binding;GTPase activity;GTP binding