GLIPR2

GLI pathogenesis related 2, the group of CAP superfamily

Basic information

Region (hg38): 9:36136536-36163913

Previous symbols: [ "C9orf19" ]

Links

ENSG00000122694 ∙ NCBI:152007 ∙ OMIM:607141 ∙ HGNC:18007 ∙ Uniprot:Q9H4G4 ∙ 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 GLIPR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLIPR2 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				1	1	2
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	17	3	1

Variants in GLIPR2

This is a list of pathogenic ClinVar variants found in the GLIPR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-36136840-C-T			Likely benign (Mar 01, 2023)
9-36136852-C-A			Likely benign (Feb 01, 2023)
9-36147797-T-C		not specified	Uncertain significance (Dec 15, 2024)
9-36147801-A-C		not specified	Uncertain significance (Oct 13, 2021)
9-36147817-G-T		not specified	Uncertain significance (Dec 23, 2024)
9-36147831-A-G		not specified	Uncertain significance (Aug 02, 2021)
9-36147849-T-C		not specified	Uncertain significance (Jan 25, 2023)
9-36147855-C-A		not specified	Uncertain significance (Feb 10, 2025)
9-36147855-C-G		not specified	Uncertain significance (Jul 15, 2021)
9-36147874-C-T			Benign (Oct 10, 2018)
9-36147884-G-A		not specified	Uncertain significance (Jan 26, 2023)
9-36148551-T-C		not specified	Uncertain significance (Dec 01, 2022)
9-36148570-C-T		not specified	Uncertain significance (Feb 27, 2025)
9-36150914-A-C		not specified	Uncertain significance (Feb 26, 2025)
9-36162376-A-G		not specified	Uncertain significance (Jul 30, 2024)
9-36162378-G-A		not specified	Uncertain significance (Jun 22, 2024)
9-36162379-G-T		not specified	Uncertain significance (Jul 25, 2023)
9-36162386-A-T		not specified	Uncertain significance (Jul 07, 2022)
9-36162429-C-T			Benign/Likely benign (Mar 01, 2023)
9-36162439-T-G		not specified	Uncertain significance (May 23, 2024)
9-36162448-G-A		not specified	Uncertain significance (Nov 10, 2024)
9-36162493-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-36162502-G-A		not specified	Uncertain significance (Sep 27, 2022)
9-36162509-C-T		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLIPR2	protein_coding	protein_coding	ENST00000377960	5	27179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000486	0.440	125543	0	205	125748	0.000815

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.307	87	95.4	0.912	0.00000591	1018
Missense in Polyphen		26	31.284	0.83108		328
Synonymous	-0.0665	42	41.5	1.01	0.00000300	272
Loss of Function	0.344	7	8.05	0.869	3.41e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00710	0.00700
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000991	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.720
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.466
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glipr2

Gene ontology

• Biological process: positive regulation of epithelial cell migration;positive regulation of epithelial to mesenchymal transition;positive regulation of ERK1 and ERK2 cascade
• Cellular component: Golgi membrane;extracellular space;extracellular exosome
• Molecular function: protein homodimerization activity