GPC2

protein-coding

glypican 2, the group of Glypicans

Gene summary

Predicted to be involved in several processes, including positive regulation of neuron projection development; regulation of protein localization to membrane; and smoothened signaling pathway. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152742.3

Inheritance

—

ClinVar variants

U:88B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr7:100,169,606-100,177,381

External References & Databases

Ensembl (ENSG00000213420)

Transcript & Mutation Effects

hg38 • Region Span ~7.8 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 GPC2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 92

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152742.3. 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			1 clinvar	1 clinvar		2
missense			87 clinvar	6 clinvar		93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	88	7	0	95

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152742.3	RefSeq	NP_689955.1	10	MANE Select
ENST00000292377.4	Ensembl	ENSP00000292377.2	10	MANE Select
ENST00000480087.5	Ensembl	ENSP00000488396.1	3	Standard
ENST00000893618.1	Ensembl	ENSP00000563677.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
Metabolism of fat-soluble vitamins
Metabolism of carbohydrates
A tetrasaccharide linker sequence is required for GAG synthesis

Biological Process

retinoid metabolic process
glycosaminoglycan biosynthetic process
glycosaminoglycan catabolic process
smoothened signaling pathway
regulation of signal transduction

Molecular Function

protein binding

Cellular Component

extracellular space
endoplasmic reticulum
Golgi lumen
plasma membrane
lysosomal lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000292377
Coding exons: 10
Length: 7767
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	262	312	0.839	0.0000178	3565
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00014	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000074	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: -0.87
RVIS percentile EVS: 10.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0988

Gene Damage Prediction

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