GPA33

glycoprotein A33, the group of V-set domain containing|IgCAM CXADR-related subfamily|Immunoglobulin like domain containing

Basic information

Region (hg38): 1:167052836-167166479

Links

ENSG00000143167 ∙ NCBI:10223 ∙ OMIM:602171 ∙ HGNC:4445 ∙ Uniprot:Q99795 ∙ 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 GPA33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPA33 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			18	3	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	1

Variants in GPA33

This is a list of pathogenic ClinVar variants found in the GPA33 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167054342-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-167054353-G-A		not specified	Uncertain significance (Mar 28, 2024)
1-167054443-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-167054453-A-T		not specified	Uncertain significance (Nov 27, 2023)
1-167055088-C-T		not specified	Uncertain significance (Jun 21, 2022)
1-167055097-C-T			Likely benign (May 10, 2018)
1-167055108-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-167055742-C-T		not specified	Uncertain significance (May 11, 2022)
1-167055807-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-167063658-C-A			Benign (Apr 24, 2018)
1-167063671-G-T		not specified	Uncertain significance (Mar 28, 2024)
1-167063674-A-G		not specified	Uncertain significance (Jan 11, 2023)
1-167063713-C-A		not specified	Uncertain significance (May 03, 2023)
1-167063714-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-167068942-C-T		not specified	Uncertain significance (May 24, 2024)
1-167068943-G-A			Likely benign (May 10, 2018)
1-167069040-A-T		not specified	Uncertain significance (Mar 07, 2023)
1-167069042-C-T		not specified	Uncertain significance (Jan 24, 2024)
1-167069075-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-167069104-T-G		not specified	Uncertain significance (Jun 13, 2024)
1-167069119-G-C		not specified	Uncertain significance (Oct 05, 2022)
1-167069123-A-G		not specified	Uncertain significance (Jun 03, 2022)
1-167069125-A-G		not specified	Likely benign (Sep 20, 2023)
1-167073386-G-A		not specified	Uncertain significance (Jan 10, 2022)
1-167073452-G-A		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPA33	protein_coding	protein_coding	ENST00000367868	7	37796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000355	0.818	125587	0	161	125748	0.000640

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00811	198	198	0.998	0.0000119	2067
Missense in Polyphen		53	59.291	0.8939		640
Synonymous	-1.61	103	84.2	1.22	0.00000572	622
Loss of Function	1.36	11	17.0	0.646	9.91e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00134
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.00511	0.00512
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00511	0.00512
South Asian	0.000654	0.000555
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cell-cell recognition and signaling.

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• loftool: 0.850
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.112

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpa33
• 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); hematopoietic system phenotype; neoplasm; digestive/alimentary phenotype; immune system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: plasma membrane;integral component of plasma membrane;extracellular exosome
• Molecular function: protein binding;signaling receptor activity