GP2

glycoprotein 2

Basic information

Region (hg38): 16:20309574-20327808

Links

ENSG00000169347 ∙ NCBI:2813 ∙ OMIM:602977 ∙ HGNC:4441 ∙ Uniprot:P55259 ∙ 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 GP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GP2 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	2	3
missense			38	4	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	38	5	3

Variants in GP2

This is a list of pathogenic ClinVar variants found in the GP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20311266-C-A		not specified	Uncertain significance (Dec 19, 2023)
16-20311279-A-G		not specified	Uncertain significance (Jan 27, 2022)
16-20311280-C-A			Benign (Jan 30, 2018)
16-20314690-G-C		not specified	Uncertain significance (Nov 21, 2024)
16-20315962-G-A		not specified	Uncertain significance (Dec 06, 2021)
16-20315999-G-A			Benign (Jan 30, 2018)
16-20316016-T-C		not specified	Uncertain significance (Apr 05, 2023)
16-20317215-G-A		not specified	Uncertain significance (Jan 06, 2023)
16-20317232-A-G		not specified	Uncertain significance (Feb 05, 2024)
16-20317259-T-C		not specified	Uncertain significance (Feb 28, 2024)
16-20317322-G-C		not specified	Uncertain significance (Jan 03, 2024)
16-20317344-C-T			Benign (Feb 24, 2021)
16-20318204-A-G		not specified	Uncertain significance (Feb 12, 2025)
16-20318269-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-20318303-C-T		not specified	Uncertain significance (Mar 07, 2024)
16-20318312-C-T		not specified	Likely benign (Jan 31, 2022)
16-20318408-C-T		not specified	Uncertain significance (Feb 06, 2024)
16-20318419-A-G		not specified	Uncertain significance (Jan 07, 2025)
16-20318420-C-T		not specified	Likely benign (Jan 01, 2025)
16-20318421-G-A			Likely benign (May 18, 2018)
16-20319689-A-G		not specified	Uncertain significance (Sep 02, 2024)
16-20319692-T-C		not specified	Uncertain significance (Nov 11, 2024)
16-20319720-C-A		not specified	Uncertain significance (Jan 18, 2025)
16-20319722-T-C		not specified	Likely benign (Feb 13, 2025)
16-20319726-C-T		not specified	Uncertain significance (Aug 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GP2	protein_coding	protein_coding	ENST00000381362	11	18237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-21	0.000758	125573	1	173	125747	0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.696	274	308	0.888	0.0000164	3523
Missense in Polyphen		67	91.152	0.73504		1118
Synonymous	-1.23	137	120	1.14	0.00000647	1040
Loss of Function	-0.249	31	29.5	1.05	0.00000167	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00169
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00120	0.00120
European (Non-Finnish)	0.000752	0.000739
Middle Eastern	0.000218	0.000217
South Asian	0.000359	0.000359
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.103
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.371
• hipred: N
• hipred_score: 0.146
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gp2
• Phenotype: normal phenotype

Gene ontology

• Cellular component: extracellular region;plasma membrane;anchored component of membrane;extracellular exosome