TPD52

protein-coding

tumor protein D52

Gene summary

Enables calcium ion binding activity and protein homodimerization activity. Involved in B cell differentiation. Located in endoplasmic reticulum and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001025253.3

Inheritance

—

ClinVar variants

U:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr8:80,034,745-80,231,232

External References & Databases

Ensembl (ENSG00000076554)

Transcript & Mutation Effects

hg38 • Region Span ~196.5 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 TPD52 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001025253.3. 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						0
missense			20 clinvar			20
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	27	0	0	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001025253.3	RefSeq	NP_001020424.1	8	MANE Select
ENST00000518937.6	Ensembl	ENSP00000429915.1	8	MANE Select
NM_001025252.3	RefSeq	NP_001020423.1	6	Standard
NM_001287140.2	RefSeq	NP_001274069.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Golgi Associated Vesicle Biogenesis
Clathrin derived vesicle budding
trans-Golgi Network Vesicle Budding
Vesicle-mediated transport
Membrane Trafficking

Biological Process

anatomical structure morphogenesis
B cell differentiation
secretion

Molecular Function

calcium ion binding
protein binding
protein homodimerization activity
protein heterodimerization activity

Cellular Component

cytoplasm
endoplasmic reticulum
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379097
Coding exons: 6
Length: 272897
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125745
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.901	88	115	0.764	0.00000586	1427
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0986

Intolerance Scores

LoFtool: 0.908
RVIS EVS: 0.33
RVIS percentile EVS: 73.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.731

Gene Damage Prediction

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