GPC2

glypican 2, the group of Glypicans

Basic information

Region (hg38): 7:100169606-100177381

Links

ENSG00000213420 ∙ NCBI:221914 ∙ OMIM:618446 ∙ HGNC:4450 ∙ Uniprot:Q8N158 ∙ 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 GPC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPC2 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			55	5		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	5	0

Variants in GPC2

This is a list of pathogenic ClinVar variants found in the GPC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100170234-C-T		not specified	Uncertain significance (Jun 28, 2023)
7-100170271-T-A		not specified	Uncertain significance (May 30, 2023)
7-100170298-T-G		not specified	Uncertain significance (Nov 10, 2022)
7-100170303-G-A		not specified	Uncertain significance (Sep 13, 2023)
7-100170310-C-G		not specified	Uncertain significance (Jun 11, 2024)
7-100170310-C-T		not specified	Uncertain significance (Dec 16, 2023)
7-100170321-C-T		not specified	Uncertain significance (Apr 28, 2022)
7-100170385-G-A		not specified	Uncertain significance (Dec 10, 2024)
7-100170405-C-T		not specified	Uncertain significance (Sep 26, 2024)
7-100170420-A-C		not specified	Likely benign (Nov 18, 2022)
7-100170469-C-T		not specified	Uncertain significance (Jan 20, 2025)
7-100170478-C-T		not specified	Uncertain significance (Jul 10, 2024)
7-100171291-G-C		not specified	Uncertain significance (Sep 13, 2023)
7-100171315-T-G		not specified	Uncertain significance (Jul 13, 2021)
7-100171320-G-A		not specified	Uncertain significance (Nov 14, 2024)
7-100171344-C-T		not specified	Uncertain significance (Feb 28, 2025)
7-100171408-G-C		not specified	Uncertain significance (Feb 02, 2022)
7-100171419-A-G		not specified	Uncertain significance (Aug 17, 2021)
7-100171425-G-A		not specified	Uncertain significance (Oct 30, 2023)
7-100171543-C-T		not specified	Uncertain significance (May 01, 2024)
7-100171569-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-100171581-G-A		not specified	Uncertain significance (Dec 12, 2023)
7-100171596-A-C		not specified	Uncertain significance (Dec 11, 2023)
7-100171617-G-A		not specified	Uncertain significance (Feb 28, 2024)
7-100171627-G-C		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPC2	protein_coding	protein_coding	ENST00000292377	10	7767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0315	0.968	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	262	312	0.839	0.0000178	3565
Missense in Polyphen		98	117.93	0.83102		1404
Synonymous	0.873	120	133	0.904	0.00000707	1288
Loss of Function	3.12	7	23.3	0.301	0.00000125	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.000139	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000744	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface proteoglycan that bears heparan sulfate. May fulfill a function related to the motile behaviors of developing neurons (By similarity). {ECO:0000250}.
• Pathway: Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;HS-GAG biosynthesis;HS-GAG degradation;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism;Metabolism of vitamins and cofactors;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling;Glypican 2 network (Consensus)

Intolerance Scores

• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.65

Haploinsufficiency Scores

• pHI: 0.111
• hipred: Y
• hipred_score: 0.625
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpc2
• Phenotype: renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: retinoid metabolic process;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;smoothened signaling pathway;regulation of signal transduction;neuron differentiation
• Cellular component: extracellular space;endoplasmic reticulum;Golgi lumen;plasma membrane;lysosomal lumen;anchored component of plasma membrane;collagen-containing extracellular matrix
• Molecular function: protein binding