GNL1

G protein nucleolar 1 (putative)

Basic information

Region (hg38): 6:30541380-30556489

Links

ENSG00000204590 ∙ NCBI:2794 ∙ OMIM:143024 ∙ HGNC:4413 ∙ Uniprot:P36915 ∙ 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 GNL1 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNL1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in GNL1

This is a list of pathogenic ClinVar variants found in the GNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30546078-C-A		not specified	Uncertain significance (May 18, 2023)
6-30546124-G-C		not specified	Uncertain significance (Feb 28, 2024)
6-30546242-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-30546272-A-C		not specified	Uncertain significance (Feb 22, 2023)
6-30546717-G-C		not specified	Uncertain significance (Apr 19, 2023)
6-30546741-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-30546758-C-T		not specified	Uncertain significance (Jul 06, 2021)
6-30547140-G-T		not specified	Uncertain significance (Jul 19, 2023)
6-30547196-C-T		not specified	Uncertain significance (Jan 02, 2024)
6-30547244-T-G		not specified	Uncertain significance (Jan 06, 2023)
6-30547393-G-C		not specified	Uncertain significance (Mar 31, 2023)
6-30547495-C-T		not specified	Uncertain significance (May 24, 2023)
6-30552628-C-T		not specified	Uncertain significance (Apr 25, 2022)
6-30553131-C-G		not specified	Uncertain significance (Jul 06, 2021)
6-30553141-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-30553430-T-C		not specified	Uncertain significance (Jul 30, 2023)
6-30554826-G-A		not specified	Uncertain significance (Oct 24, 2023)
6-30554844-G-A		not specified	Uncertain significance (Jul 08, 2022)
6-30555064-G-T		not specified	Uncertain significance (Jan 18, 2022)
6-30555147-C-T		not specified	Uncertain significance (Feb 15, 2023)
6-30555573-C-G		not specified	Uncertain significance (Dec 28, 2022)
6-30555577-G-C		not specified	Uncertain significance (Nov 06, 2023)
6-30555684-C-T		not specified	Uncertain significance (Sep 20, 2023)
6-30556143-C-G		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNL1	protein_coding	protein_coding	ENST00000376621	12	15798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000721	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	225	354	0.636	0.0000204	3895
Missense in Polyphen		53	104.84	0.50551		1134
Synonymous	0.650	129	139	0.930	0.00000755	1220
Loss of Function	4.94	3	34.1	0.0879	0.00000185	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible regulatory or functional link with the histocompatibility cluster.

Intolerance Scores

• loftool: 0.149
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• pHI: 0.552
• hipred: Y
• hipred_score: 0.675
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnl1

Gene ontology

• Biological process: T cell mediated immunity;cellular response to DNA damage stimulus;signal transduction
• Cellular component: extracellular space;nucleus
• Molecular function: structural molecule activity;GTP binding