TPD52

tumor protein D52

Basic information

Region (hg38): 8:80034745-80231232

Links

ENSG00000076554 ∙ NCBI:7163 ∙ OMIM:604068 ∙ HGNC:12005 ∙ Uniprot:P55327 ∙ 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 TPD52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPD52 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2			2
Total	0	0	6	0	0

Variants in TPD52

This is a list of pathogenic ClinVar variants found in the TPD52 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-80038123-C-T		not specified	Uncertain significance (Jul 07, 2022)
8-80038243-A-G			Benign (Aug 09, 2017)
8-80051564-C-T		not specified	Uncertain significance (Feb 08, 2023)
8-80051566-G-A		not specified	Uncertain significance (May 30, 2024)
8-80051570-A-C		not specified	Uncertain significance (Feb 15, 2023)
8-80053316-C-T		not specified	Uncertain significance (Jan 11, 2023)
8-80053361-G-A		not specified	Uncertain significance (Jun 28, 2023)
8-80064518-G-A		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPD52	protein_coding	protein_coding	ENST00000379097	6	272897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000849	0.789	125731	0	14	125745	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.901	88	115	0.764	0.00000586	1427
Missense in Polyphen		23	36.495	0.63022		504
Synonymous	0.788	41	47.9	0.855	0.00000284	439
Loss of Function	1.16	8	12.4	0.645	6.19e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000200	0.000200
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.321
• hipred: N
• hipred_score: 0.216
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpd52

Gene ontology

• Biological process: anatomical structure morphogenesis;B cell differentiation;secretion
• Cellular component: cytoplasm;endoplasmic reticulum;perinuclear region of cytoplasm
• Molecular function: calcium ion binding;protein binding;protein homodimerization activity;protein heterodimerization activity