GNL1

protein-coding

G protein nucleolar 1 (putative)

Gene summary

The GNL1 gene, identified in the human major histocompatibility complex class I region, shows a high degree of similarity with its mouse counterpart. The GNL1 gene is located less than 2 kb centromeric to HLA-E, in the same transcriptional orientation. GNL1 is telomeric to HLA-B and HLA-C. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005275.5

Inheritance

—

ClinVar variants

U:69B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr6:30,541,381-30,556,489

External References & Databases

Ensembl (ENSG00000204590)

Transcript & Mutation Effects

hg38 • Region Span ~15.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GNL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 59

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005275.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			65 clinvar	2 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	69	2	0	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005275.5	RefSeq	NP_005266.2	12	MANE Select
ENST00000376621.8	Ensembl	ENSP00000365806.3	12	MANE Select
ENST00000433809.1	Ensembl	ENSP00000404728.1	5	Standard
ENST00000863388.1	Ensembl	ENSP00000533447.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

T cell mediated immunity
cellular response to DNA damage stimulus
signal transduction

Molecular Function

structural molecule activity
GTP binding

Cellular Component

extracellular space
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376621
Coding exons: 12
Length: 15798
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.44	225	354	0.636	0.0000204	3895
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.141

Gene Damage Prediction

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