TPD52L3

Summary

TPD52L3 (TPD52 like 3, HGNC:23382) is a protein-coding gene on chromosome 9p24.1, encoding Tumor protein D55 (Q96J77).

This gene encodes a member of the tumor protein D52-like family of proteins. These proteins are characterized by an N-terminal coiled-coil motif that is used to form homo- and heteromeric complexes with other tumor protein D52-like proteins. The encoded protein may play a role in spermatogenesis. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 89882 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_001001874

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23382
Approved symbol	TPD52L3
Name	TPD52 like 3
Location	9p24.1
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP25, D55, TPD55
Ensembl gene	ENSG00000170777
Ensembl biotype	protein_coding
OMIM	617567
Entrez	89882

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000314556, ENST00000344545, ENST00000381428

RefSeq mRNA: 3 — MANE Select: NM_001001874 NM_001001874, NM_001001875, NM_033516

CCDS: CCDS34984, CCDS34985, CCDS34986

Canonical transcript exons

ENST00000314556 — 2 exons

Exon	Start	End
ENSE00001165143	6328375	6328962
ENSE00001272769	6330976	6331891

Expression profiles

Bgee: expression breadth broad, 36 present calls, max score 98.92.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5074 / max 480.4055, expressed in 6 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
95987	0.4346	5
95986	0.0728	4

Top tissues by expression

172 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.92	gold quality
left testis	UBERON:0004533	96.90	gold quality
right testis	UBERON:0004534	96.72	gold quality
testis	UBERON:0000473	94.23	gold quality
adult organism	UBERON:0007023	92.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.05	gold quality
kidney epithelium	UBERON:0004819	87.14	gold quality
upper arm skin	UBERON:0004263	83.66	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	81.33	gold quality
nasal cavity epithelium	UBERON:0005384	80.35	gold quality
parotid gland	UBERON:0001831	78.72	gold quality
cardiac muscle of right atrium	UBERON:0003379	78.27	gold quality
myocardium	UBERON:0002349	78.21	gold quality
epithelial cell of pancreas	CL:0000083	77.91	gold quality
left ventricle myocardium	UBERON:0006566	77.82	gold quality
vastus lateralis	UBERON:0001379	76.67	gold quality
vena cava	UBERON:0004087	75.80	gold quality
quadriceps femoris	UBERON:0001377	75.02	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	73.69	gold quality
body of tongue	UBERON:0011876	73.37	gold quality
tongue	UBERON:0001723	71.68	gold quality
pons	UBERON:0000988	71.60	silver quality
inferior vagus X ganglion	UBERON:0005363	71.37	gold quality
cardia of stomach	UBERON:0001162	71.04	gold quality
nipple	UBERON:0002030	70.79	gold quality
superior surface of tongue	UBERON:0007371	70.73	gold quality
pylorus	UBERON:0001166	70.72	gold quality
trachea	UBERON:0003126	70.65	gold quality
substantia nigra pars reticulata	UBERON:0001966	70.63	silver quality
pericardium	UBERON:0002407	70.59	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting TPD52L3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Trpd52l3	ENSMUSG00000024815
rattus_norvegicus	Tpd52l3	ENSRNOG00000042441
drosophila_melanogaster	CG5174	FBGN0034345
caenorhabditis_elegans		WBGENE00008745

Paralogs (3): TPD52 (ENSG00000076554), TPD52L2 (ENSG00000101150), TPD52L1 (ENSG00000111907)

Protein

Protein identifiers

Tumor protein D55 — Q96J77 (reviewed: Q96J77)

Alternative names: Testis development protein NYD-SP25, Tumor protein D52-like 3

All UniProt accessions (1): Q96J77

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with TPD52L2.

Tissue specificity. Specifically expressed in testis. Expressed at 5.6-fold higher levels in adult testis than in fetal testis.

Similarity. Belongs to the TPD52 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96J77-1	1	yes
Q96J77-2	2
Q96J77-3	3

RefSeq proteins (3): NP_001001874, NP_001001875, NP_277051 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007327	TPD52	Family

Pfam: PF04201

UniProt features (8 total): splice variant 2, chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96J77-F1	73.00	0.20

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): FXR_IR1_Q6, FOXO4_01, FOXO1_01, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, AKT_UP_MTOR_DN.V1_UP, AKT_UP.V1_UP, ESC_J1_UP_EARLY.V1_DN, NFKBIA_TARGET_GENES, MIR570_3P, MIR5688, MIR495_3P, MIR1468_3P, MIR3065_5P, MIR1283

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TPD52L3	PDIK1L	Q8N165	453
TPD52L3	SPACA7	Q96KW9	444
TPD52L3	CCDC89	Q8N998	393
TPD52L3	CIMIP4	O43247	375
TPD52L3	CFAP276	Q5T5A4	359
TPD52L3	MEMO1	Q9Y316	334
TPD52L3	ITIH2	P19823	327
TPD52L3	MFSD6L	Q8IWD5	326
TPD52L3	PAFAH1B2	P68402	322
TPD52L3	MTMR2	Q13614	319
TPD52L3	IFT74	Q96LB3	318
TPD52L3	EIF3H	O15372	312
TPD52L3	FNDC8	Q8TC99	289
TPD52L3	WDR47	O94967	284
TPD52L3	CATSPERZ	Q9NTU4	275

IntAct

20 interactions, top by confidence:

A	B	Type	Score
AGTRAP	TPD52L3	psi-mi:“MI:0915”(physical association)	0.560
CMTM5	TPD52L3	psi-mi:“MI:0915”(physical association)	0.560
TPD52L3	AGTRAP	psi-mi:“MI:0915”(physical association)	0.560
TPD52L3	TPD52L2	psi-mi:“MI:0914”(association)	0.530
TPD52L3	TPD52L2	psi-mi:“MI:0407”(direct interaction)	0.440
TPD52L2	TPD52L3	psi-mi:“MI:0407”(direct interaction)	0.440
TPD52L3	H3-4	psi-mi:“MI:0915”(physical association)	0.400
TPD52L3	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
TPD52L3	H1-5	psi-mi:“MI:0915”(physical association)	0.400
NFIC	TPD52L3	psi-mi:“MI:0915”(physical association)	0.370
TPD52	TPD52L3	psi-mi:“MI:0915”(physical association)	0.000
TPD52L1	TPD52L3	psi-mi:“MI:0915”(physical association)	0.000
TPD52L3	TPD52L3	psi-mi:“MI:0915”(physical association)	0.000
TPD52L3	DKFZp686A1765	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): TPD52L3 (Two-hybrid), CMTM5 (Two-hybrid), TPD52L3 (Two-hybrid), TPD52L3 (Two-hybrid), TPD52L3 (Proximity Label-MS), TPD52L3 (Proximity Label-MS), TPD52L3 (Proximity Label-MS), TPD52L3 (Two-hybrid), TPD52L3 (Two-hybrid), GABPB1 (Affinity Capture-MS), GABPA (Affinity Capture-MS), TPD52 (Affinity Capture-MS), TPD52L1 (Affinity Capture-MS), TPD52L2 (Affinity Capture-MS), MYO18A (Affinity Capture-MS)

ESM2 similar proteins: A0A1L1SUL6, A1A4P9, A6NJR5, A6NNV3, A7VL23, B2RXH8, B7ZW38, D4A693, K7N6K2, O54818, O70593, O95568, P0CW24, P0DMR1, P0DV79, P51878, P55327, Q06GP8, Q16890, Q1ACD6, Q1ACD7, Q2HJ93, Q2M2D7, Q2YEM8, Q3KPR1, Q3SZ27, Q49AS3, Q4AC99, Q52LC2, Q5D7H7, Q5D7I1, Q5NVS6, Q5R387, Q62393, Q6EIX2, Q6UXV4, Q7YRC0, Q864V5, Q86UD7, Q8BJU0

Diamond homologs: O43399, O54818, P55326, P55327, Q16890, Q5RCT1, Q62393, Q6PCT3, Q95212, Q96J77, Q9CYZ2, Q9I8F4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

26 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

199 predictions. Top by Δscore:

Variant	Effect	Δscore
9:6328983:TCCA:T	donor_gain	0.9700
9:6328916:G:GT	donor_gain	0.9200
9:6329726:T:TA	donor_gain	0.9000
9:6329727:A:AA	donor_gain	0.9000
9:6328996:G:GT	donor_gain	0.8800
9:6328930:TGAAG:T	donor_gain	0.7500
9:6328934:G:GT	donor_gain	0.7500
9:6329192:C:CG	donor_gain	0.6800
9:6330323:A:AG	acceptor_gain	0.6600
9:6329187:T:A	donor_gain	0.5900
9:6329273:AAGTG:A	donor_gain	0.5800
9:6329180:C:G	donor_gain	0.5700
9:6329724:G:GA	donor_gain	0.5700
9:6330176:TTTTA:T	acceptor_loss	0.5700
9:6330177:TTTAG:T	acceptor_loss	0.5700
9:6330178:TTAGG:T	acceptor_loss	0.5700
9:6330179:TA:T	acceptor_loss	0.5700
9:6330180:A:C	acceptor_loss	0.5700
9:6330181:G:GA	acceptor_loss	0.5700
9:6330324:A:G	acceptor_gain	0.5600
9:6329179:A:AG	donor_gain	0.5200
9:6330153:CTTAA:C	acceptor_loss	0.5200
9:6330156:A:AG	acceptor_loss	0.5200
9:6330167:T:TA	acceptor_loss	0.5200
9:6330154:TTAAC:T	acceptor_loss	0.5100
9:6330155:TAACT:T	acceptor_loss	0.5100
9:6330171:CTTCT:C	acceptor_loss	0.5100
9:6330172:TTCTT:T	acceptor_loss	0.5100
9:6330173:TCTTT:T	acceptor_loss	0.5100
9:6330180:A:AG	acceptor_gain	0.5100

AlphaMissense

865 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:6328778:G:C	K61N	0.696
9:6328778:G:T	K61N	0.696
9:6328947:T:C	F118L	0.691
9:6328949:C:A	F118L	0.691
9:6328949:C:G	F118L	0.691
9:6328753:A:T	K53I	0.667
9:6328754:A:C	K53N	0.623
9:6328754:A:T	K53N	0.623
9:6328934:G:C	K113N	0.581
9:6328934:G:T	K113N	0.581
9:6328735:G:C	R47P	0.580

dbSNP variants (sampled 300 via entrez): RS1000132401 (9:6332300 G>A), RS1000784367 (9:6330011 A>T), RS1001062293 (9:6326397 G>C), RS1001353391 (9:6331431 T>C), RS1002009368 (9:6329018 ACTGT>A), RS1003163871 (9:6327284 G>A), RS1003448805 (9:6328024 T>C), RS1004464017 (9:6330527 G>C), RS1004736804 (9:6326591 A>G), RS1004756831 (9:6330832 C>A,G), RS1005350510 (9:6329503 A>G), RS1005572895 (9:6331670 G>C,T), RS1005687187 (9:6331480 G>A,T), RS1005895125 (9:6327348 T>A,C), RS1006857601 (9:6327602 T>G)

Disease associations

OMIM: gene MIM:617567 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST001588_15	Periodontal microbiota	3.000000e-06
GCST005213_5	Asthma (childhood onset)	3.000000e-08
GCST007563_32	Allergic disease (asthma, hay fever or eczema)	4.000000e-08
GCST007564_32	Asthma or allergic disease (pleiotropy)	4.000000e-22
GCST008916_20	Asthma	5.000000e-36
GCST008916_26	Asthma	3.000000e-64
GCST008916_47	Asthma	2.000000e-08
GCST008916_5	Asthma	7.000000e-17
GCST008916_83	Asthma	1.000000e-08
GCST008916_9	Asthma	4.000000e-18
GCST009391_235	Metabolite levels	5.000000e-06
GCST009798_28	Asthma	4.000000e-18
GCST009798_8	Asthma	5.000000e-67
GCST010083_249	Hemoglobin levels	3.000000e-09
GCST90002382_270	Eosinophil percentage of white cells	6.000000e-11
GCST90002403_603	Red blood cell count	5.000000e-16

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0010493	glycodeoxycholate measurement
EFO:0004509	hemoglobin measurement
EFO:0007991	eosinophil percentage of leukocytes
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
perfluorooctanoic acid	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, decreases expression	1
Estradiol	increases expression	1
Fenfluramine	increases expression	1
Malathion	decreases expression	1
Silicon Dioxide	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.