GLIPR1

GLI pathogenesis related 1, the group of GLIPR family

Basic information

Region (hg38): 12:75480753-75503863

Links

ENSG00000139278 ∙ NCBI:11010 ∙ OMIM:602692 ∙ HGNC:17001 ∙ Uniprot:P48060 ∙ 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 GLIPR1 gene.

• not_specified (32 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLIPR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006851.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			28	4		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	28	4	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLIPR1	protein_coding	protein_coding	ENST00000266659	6	23174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.07e-14	0.00438	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.182	141	147	0.958	0.00000767	1734
Missense in Polyphen		51	55.365	0.92116		626
Synonymous	-1.65	66	51.0	1.29	0.00000265	503
Loss of Function	-0.796	19	15.6	1.22	9.48e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00105
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000164	0.000163
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0827

Intolerance Scores

• loftool: 0.901
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.0495
• hipred: N
• hipred_score: 0.146
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glipr1
• Phenotype: cellular phenotype; neoplasm

Gene ontology

• Biological process: regulation of lipid metabolic process;neutrophil degranulation
• Cellular component: extracellular space;plasma membrane;membrane;integral component of membrane;azurophil granule membrane