TDRD10

Summary

TDRD10 (tudor domain containing 10, HGNC:25316) is a protein-coding gene on chromosome 1q21.3, encoding Tudor domain-containing protein 10 (Q5VZ19).

Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be active in membrane and mitochondrion.

Source: NCBI Gene 126668 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 59 total — 1 pathogenic
• MANE Select transcript: NM_182499

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25316
Approved symbol	TDRD10
Name	tudor domain containing 10
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434M202
Ensembl gene	ENSG00000163239
Ensembl biotype	protein_coding
Entrez	126668

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000368480, ENST00000368482, ENST00000462871, ENST00000468714, ENST00000479937, ENST00000889281

RefSeq mRNA: 2 — MANE Select: NM_182499 NM_001098475, NM_182499

CCDS: CCDS30878, CCDS41406

Canonical transcript exons

ENST00000368482 — 13 exons

Exon	Start	End
ENSE00001447240	154502219	154503029
ENSE00001603845	154521323	154521479
ENSE00001614154	154520304	154520374
ENSE00001638303	154508423	154508481
ENSE00001723952	154507241	154507320
ENSE00001753844	154506877	154506905
ENSE00003475572	154547409	154547479
ENSE00003532456	154542024	154542066
ENSE00003540319	154542731	154542821
ENSE00003580862	154547678	154548147
ENSE00003642189	154544372	154544517
ENSE00003654698	154543963	154544110
ENSE00003690982	154544795	154544949

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 97.28.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0939 / max 51.8748, expressed in 21 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5519	0.0410	13
5521	0.0325	7
5520	0.0203	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	97.28	gold quality
right testis	UBERON:0004534	97.25	gold quality
sperm	CL:0000019	94.77	gold quality
testis	UBERON:0000473	94.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.98	gold quality
apex of heart	UBERON:0002098	87.98	gold quality
right lobe of thyroid gland	UBERON:0001119	87.87	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.02	gold quality
left lobe of thyroid gland	UBERON:0001120	86.26	gold quality
omental fat pad	UBERON:0010414	86.16	gold quality
peritoneum	UBERON:0002358	86.09	gold quality
right ovary	UBERON:0002118	85.92	gold quality
left ovary	UBERON:0002119	85.07	gold quality
adipose tissue of abdominal region	UBERON:0007808	84.98	gold quality
thyroid gland	UBERON:0002046	84.84	gold quality
right lung	UBERON:0002167	83.98	gold quality
left ventricle myocardium	UBERON:0006566	83.32	gold quality
cardiac muscle of right atrium	UBERON:0003379	83.29	gold quality
upper lobe of left lung	UBERON:0008952	83.19	gold quality
upper lobe of lung	UBERON:0008948	82.14	gold quality
left uterine tube	UBERON:0001303	81.79	gold quality
spleen	UBERON:0002106	81.72	gold quality
right atrium auricular region	UBERON:0006631	81.56	gold quality
cardiac atrium	UBERON:0002081	81.20	gold quality
ovary	UBERON:0000992	80.91	gold quality
heart left ventricle	UBERON:0002084	80.30	gold quality
subcutaneous adipose tissue	UBERON:0002190	80.27	gold quality
cardiac ventricle	UBERON:0002082	79.91	gold quality
right adrenal gland cortex	UBERON:0035827	79.32	gold quality
right adrenal gland	UBERON:0001233	79.25	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.25
E-MTAB-6678	no	2.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting TDRD10, 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-548P	99.98	72.25	3784
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-136-5P	99.50	67.26	1153
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-6794-3P	98.76	66.99	894
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-4664-5P	98.17	65.07	1020
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-3936	97.64	64.47	732
HSA-MIR-4639-3P	97.54	67.12	787
HSA-MIR-342-5P	97.25	64.10	817
HSA-MIR-132-5P	96.61	65.79	115
HSA-MIR-4714-3P	96.53	67.44	452
HSA-MIR-6747-5P	96.17	64.99	743
HSA-MIR-5586-3P	95.51	67.00	805

Literature-anchored findings (GeneRIF, showing 1)

• Suggest rs6674171 TDRD10 SNP is not a susceptibility factor for abdominal aortic aneurysms in an Italian population. (PMID:24423473)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tdrkh	ENSDARG00000053474
drosophila_melanogaster	tud	FBGN0003891
drosophila_melanogaster	papi	FBGN0031401

Paralogs (6): TDRD1 (ENSG00000095627), TDRD5 (ENSG00000162782), TDRD6 (ENSG00000180113), TDRKH (ENSG00000182134), TDRD7 (ENSG00000196116), TDRD15 (ENSG00000218819)

Protein

Protein identifiers

Tudor domain-containing protein 10 — Q5VZ19 (reviewed: Q5VZ19)

All UniProt accessions (1): Q5VZ19

Isoforms (2)

UniProt ID	Names	Canonical?
Q5VZ19-1	1	yes
Q5VZ19-2	2

RefSeq proteins (2): NP_001091945, NP_872305* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR002999	Tudor	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035437	SNase_OB-fold_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR047385	RRM_TDRD10	Domain

Pfam: PF00076, PF00567

UniProt features (9 total): domain 2, sequence variant 2, sequence conflict 2, chain 1, coiled-coil region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VZ19-F1	72.71	0.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): chr1q21, GOMF_PROTEIN_KINASE_A_REGULATORY_SUBUNIT_BINDING, GOMF_PROTEIN_KINASE_A_BINDING, MYC_UP.V1_UP, ZNF92_TARGET_GENES, MIR548E_5P, MIR6077, MIR659_3P, MIR4684_5P, MIR5006_5P, MIR202_5P, MIR4664_5P, MIR4639_3P, MIR342_5P, MIR4714_3P

GO Biological Process (0):

GO Molecular Function (3): RNA binding (GO:0003723), protein kinase A regulatory subunit binding (GO:0034237), nucleic acid binding (GO:0003676)

GO Cellular Component (2): mitochondrion (GO:0005739), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
protein kinase A binding	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

302 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TDRD10	PRAC2	D3DTV9	594
TDRD10	ANKRD53	Q8N9V6	572
TDRD10	TDRD5	Q8NAT2	526
TDRD10	TMEM132C	Q8N3T6	513
TDRD10	TDRD12	Q587J7	507
TDRD10	TDRKH	Q9Y2W6	507
TDRD10	TDRD9	Q8NDG6	445
TDRD10	TDRD1	Q9BXT4	431
TDRD10	PHF20L1	A8MW92	419
TDRD10	STK31	Q9BXU1	400
TDRD10	FAM177B	A6PVY3	380
TDRD10	TDRD15	B5MCY1	370
TDRD10	TDRD7	Q8NHU6	368
TDRD10	TDRD6	O60522	350
TDRD10	ZNF154	Q13106	349

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PPM1L	TDRD10	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): TDRD10 (Proximity Label-MS), TDRD10 (Synthetic Lethality), TDRD10 (Affinity Capture-MS)

ESM2 similar proteins: A0JM98, A1L1H3, A6NAF9, A6QLE1, A9CPT4, B5MCY1, D2H0H6, D2H3M0, D4A7V9, E1BPH3, E1C3S7, E2QTD3, E2RDV1, E7FDW8, F1R237, O60522, P57075, P61407, P97874, Q14B46, Q1L981, Q4R3G4, Q58EK5, Q5DTW2, Q5JTW2, Q5M7P8, Q5RAH6, Q5VCS6, Q5VZ19, Q5XGX5, Q61846, Q68DX3, Q6NU04, Q80VK6, Q8K1H1, Q8NAT2, Q8NHU6, Q90WE3, Q99KY4, Q99MV1

Diamond homologs: A2A5N3, A5DM21, A5DW14, O13620, O43390, O60506, P11940, P20965, P29341, P61286, P78814, P92964, Q01560, Q4VXU2, Q5AI15, Q5R8F7, Q5VZ19, Q6CQR6, Q7TMK9, Q7TP47, Q8ITY4, Q8L3X8, Q8N9W6, Q8WP23, Q9EPH8, Q9FMP4, Q9H361, Q9Y4C8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	45
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2425513	NC_000001.10:g.(?153963273)(154580482_?)del	Pathogenic

SpliceAI

2671 predictions. Top by Δscore:

Variant	Effect	Δscore
1:154508417:TCTTA:T	acceptor_loss	1.0000
1:154508418:CTTAG:C	acceptor_loss	1.0000
1:154508421:A:AG	acceptor_gain	1.0000
1:154508421:AGGAT:A	acceptor_loss	1.0000
1:154508422:G:GA	acceptor_loss	1.0000
1:154508422:G:GG	acceptor_gain	1.0000
1:154508477:CTAAG:C	donor_loss	1.0000
1:154508478:TAAG:T	donor_loss	1.0000
1:154508479:AAGGT:A	donor_loss	1.0000
1:154508480:AGGTA:A	donor_loss	1.0000
1:154508481:GGT:G	donor_loss	1.0000
1:154508482:G:A	donor_loss	1.0000
1:154508483:T:A	donor_loss	1.0000
1:154521322:GCTTT:G	acceptor_gain	1.0000
1:154521478:TGGTA:T	donor_loss	1.0000
1:154521480:G:A	donor_loss	1.0000
1:154521481:T:G	donor_loss	1.0000
1:154542097:G:GT	donor_gain	1.0000
1:154542157:C:G	donor_gain	1.0000
1:154544789:T:TA	acceptor_gain	1.0000
1:154544792:CA:C	acceptor_loss	1.0000
1:154544793:A:AG	acceptor_gain	1.0000
1:154544793:AG:A	acceptor_gain	1.0000
1:154544793:AGGT:A	acceptor_gain	1.0000
1:154544794:G:GT	acceptor_gain	1.0000
1:154544794:GG:G	acceptor_gain	1.0000
1:154544794:GGT:G	acceptor_gain	1.0000
1:154544794:GGTG:G	acceptor_gain	1.0000
1:154544794:GGTGT:G	acceptor_gain	1.0000
1:154544945:GAAAG:G	donor_gain	1.0000

AlphaMissense

2311 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:154508453:T:A	V38D	0.994
1:154521328:C:A	A73E	0.991
1:154544517:G:T	R266M	0.990
1:154544795:G:C	R266S	0.985
1:154544795:G:T	R266S	0.985
1:154543997:T:C	F180L	0.984
1:154543999:C:A	F180L	0.984
1:154543999:C:G	F180L	0.984
1:154508462:T:C	L41P	0.982
1:154544517:G:C	R266T	0.982
1:154521324:T:C	F72L	0.981
1:154521326:T:A	F72L	0.981
1:154521326:T:G	F72L	0.981
1:154521330:T:C	F74L	0.981
1:154521332:T:A	F74L	0.981
1:154521332:T:G	F74L	0.981
1:154544798:T:G	C267W	0.981
1:154508462:T:A	L41H	0.980
1:154544934:T:C	F313L	0.980
1:154544936:C:A	F313L	0.980
1:154544936:C:G	F313L	0.980
1:154544012:T:A	W185R	0.976
1:154544012:T:C	W185R	0.976
1:154544796:T:C	C267R	0.976
1:154521334:T:A	V75E	0.973
1:154544510:T:A	W264R	0.973
1:154544510:T:C	W264R	0.973
1:154544090:T:A	W211R	0.972
1:154544090:T:C	W211R	0.972
1:154544833:T:A	V279D	0.970

dbSNP variants (sampled 300 via entrez): RS1000081201 (1:154501235 A>G), RS1000089918 (1:154529591 G>A), RS1000141935 (1:154524136 A>G), RS1000141997 (1:154510541 A>G), RS1000172084 (1:154506801 C>T), RS1000205450 (1:154547226 G>A), RS1000257557 (1:154504785 CAGAT>C), RS1000267933 (1:154535406 C>T), RS1000358905 (1:154541565 C>A,T), RS1000490518 (1:154545955 A>G,T), RS1000509449 (1:154505379 A>G), RS1000536320 (1:154501400 G>A,C,T), RS1000545062 (1:154548047 T>C), RS1000551432 (1:154503577 G>T), RS1000681849 (1:154511645 C>A,G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:610738

GenCC curated gene-disease

Mondo (1): Kostmann syndrome (MONDO:0012548)

Orphanet (1): Kostmann syndrome (Orphanet:99749)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002665_2	Cerebrospinal fluid levels of Alzheimer’s disease-related proteins	6.000000e-63

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004810	interleukin-6 measurement
EFO:0006514	Alzheimer’s disease biomarker measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537592	Neutropenia, Severe Congenital, Autosomal Recessive 3 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
benzo(e)pyrene	increases methylation	1
aflatoxin B2	affects methylation	1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine	increases expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00244010	Not specified	COMPLETED	Partially Matched Stem Cell Transplantation for Patients With Refractory Severe Aplastic Anemia or Refractory Cytopenias