GLIPR1

GLI pathogenesis related 1, the group of GLIPR family

Basic information

Region (hg38): 12:75480752-75503863

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.

• Inborn genetic diseases (21 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.

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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			6			6
Total	0	0	20	1	2

Variants in GLIPR1

This is a list of pathogenic ClinVar variants found in the GLIPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-75480903-T-C		not specified	Likely benign (Jan 03, 2024)
12-75480930-A-G		not specified	Likely benign (Feb 22, 2023)
12-75480964-C-G		not specified	Uncertain significance (Dec 27, 2023)
12-75481843-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-75481859-T-C		not specified	Uncertain significance (Aug 09, 2021)
12-75481887-G-A			Benign (Jan 30, 2018)
12-75481891-T-C		not specified	Uncertain significance (Aug 28, 2023)
12-75481929-C-T			Benign (Jan 30, 2018)
12-75481930-C-G		not specified	Uncertain significance (Sep 12, 2023)
12-75481943-C-T		not specified	Uncertain significance (Nov 03, 2023)
12-75490478-C-G		not specified	Uncertain significance (Aug 16, 2021)
12-75490490-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-75490493-C-T		not specified	Uncertain significance (Nov 19, 2022)
12-75490511-G-A		not specified	Uncertain significance (Feb 22, 2023)
12-75495572-T-C			Benign (Jan 30, 2018)
12-75495590-A-G		not specified	Uncertain significance (Jan 26, 2022)
12-75495600-A-G		not specified	Uncertain significance (Sep 13, 2023)
12-75495643-G-C		not specified	Uncertain significance (Sep 27, 2022)
12-75498866-G-C		not specified	Uncertain significance (Dec 06, 2022)
12-75498893-T-C		not specified	Uncertain significance (Sep 14, 2022)
12-75498925-A-G		not specified	Uncertain significance (Jun 02, 2023)
12-75499882-A-G		not specified	Uncertain significance (Mar 23, 2023)
12-75501794-C-A		not specified	Uncertain significance (Jan 10, 2023)
12-75501815-G-T		not specified	Uncertain significance (Jan 11, 2023)
12-75501928-T-C		not specified	Uncertain significance (Nov 19, 2022)

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