GPC5

glypican 5, the group of Glypicans|MicroRNA protein coding host genes

Basic information

Region (hg38): 13:91398620-92873682

Links

ENSG00000179399 ∙ NCBI:2262 ∙ OMIM:602446 ∙ HGNC:4453 ∙ Uniprot:P78333 ∙ 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 GPC5 gene.

• Inborn genetic diseases (31 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPC5 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			28	3	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	3

Variants in GPC5

This is a list of pathogenic ClinVar variants found in the GPC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-91399053-G-A		not specified	Uncertain significance (Dec 28, 2022)
13-91399066-C-A		not specified	Uncertain significance (Feb 06, 2024)
13-91399066-C-G		not specified	Likely benign (May 15, 2023)
13-91399068-G-T		not specified	Uncertain significance (Jan 23, 2023)
13-91399093-T-C		not specified	Uncertain significance (Jul 05, 2022)
13-91399113-C-A		not specified	Uncertain significance (Jan 23, 2024)
13-91399125-G-A		not specified	Uncertain significance (Jul 13, 2021)
13-91399176-G-A		not specified	Uncertain significance (Nov 30, 2022)
13-91399199-G-A			Benign (Jan 30, 2018)
13-91448836-C-T		not specified	Uncertain significance (Mar 29, 2023)
13-91448869-C-T		not specified	Uncertain significance (Sep 14, 2021)
13-91448880-A-G		not specified	Likely benign (Mar 14, 2023)
13-91448895-A-G		not specified	Uncertain significance (Sep 16, 2021)
13-91448908-C-T		not specified	Uncertain significance (Dec 07, 2021)
13-91693344-A-G			Benign (Dec 31, 2019)
13-91693381-G-C		not specified	Uncertain significance (May 04, 2022)
13-91693418-G-T		GPC5-related disorder	Likely benign (Feb 09, 2022)
13-91693427-A-G		not specified	Uncertain significance (Oct 12, 2022)
13-91693445-G-A		not specified	Uncertain significance (May 17, 2023)
13-91693591-T-G		GPC5-related disorder	Likely benign (Mar 30, 2023)
13-91693637-C-G		GPC5-related disorder	Likely benign (Mar 21, 2022)
13-91693742-C-G		not specified	Uncertain significance (Oct 03, 2022)
13-91693742-C-T		not specified	Uncertain significance (Apr 18, 2023)
13-91693760-A-G		not specified	Uncertain significance (Dec 02, 2022)
13-91693850-C-T		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPC5	protein_coding	protein_coding	ENST00000377067	8	1468562

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.99e-10	0.550	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.589	351	321	1.09	0.0000168	3738
Missense in Polyphen		127	119.51	1.0626		1480
Synonymous	-1.44	143	123	1.17	0.00000680	1125
Loss of Function	1.24	18	24.6	0.730	0.00000126	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000235	0.000229
Middle Eastern	0.000273	0.000272
South Asian	0.000726	0.000719
Other	0.000350	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface proteoglycan that bears heparan sulfate. {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;Release of Hh-Np from the secreting cell;Hedgehog ligand biogenesis;Metabolism of vitamins and cofactors;Signaling by Hedgehog;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.844
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.94

Haploinsufficiency Scores

• pHI: 0.673
• hipred: N
• hipred_score: 0.334
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpc5
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype

Gene ontology

• Biological process: retinoid metabolic process;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;regulation of signal transduction
• Cellular component: extracellular region;extracellular space;Golgi lumen;plasma membrane;integral component of membrane;lysosomal lumen;anchored component of plasma membrane;collagen-containing extracellular matrix