TDRD15

Summary

TDRD15 (tudor domain containing 15, HGNC:45037) is a protein-coding gene on chromosome 2p24.1, encoding Tudor domain-containing protein 15 (B5MCY1).

At a glance

• GWAS associations: 31
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001306137

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:45037
Approved symbol	TDRD15
Name	tudor domain containing 15
Location	2p24.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000218819
Ensembl biotype	protein_coding
Entrez	100129278

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000405799, ENST00000622654

RefSeq mRNA: 1 — MANE Select: NM_001306137 NM_001306137

CCDS: CCDS77385

Canonical transcript exons

ENST00000405799 — 4 exons

Exon	Start	End
ENSE00001549835	21134762	21134847
ENSE00001552820	21127601	21127711
ENSE00001557323	21137465	21144368
ENSE00001562954	21123968	21124046

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 83.19.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.19	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	62.27	gold quality
testis	UBERON:0000473	59.31	gold quality
right testis	UBERON:0004534	58.54	gold quality
left testis	UBERON:0004533	56.57	gold quality
liver	UBERON:0002107	55.16	gold quality
right lobe of liver	UBERON:0001114	54.50	gold quality
colonic epithelium	UBERON:0000397	45.17	gold quality
bone marrow cell	CL:0002092	44.64	gold quality
sural nerve	UBERON:0015488	39.60	gold quality
lymph node	UBERON:0000029	39.50	gold quality
vermiform appendix	UBERON:0001154	37.64	gold quality
monocyte	CL:0000576	37.54	gold quality
leukocyte	CL:0000738	37.13	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
hindlimb stylopod muscle	UBERON:0004252	36.47	silver quality
cortical plate	UBERON:0005343	36.47	gold quality
calcaneal tendon	UBERON:0003701	36.14	gold quality
endometrium	UBERON:0001295	36.13	gold quality
bone marrow	UBERON:0002371	36.07	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.76	gold quality
granulocyte	CL:0000094	34.45	gold quality
muscle tissue	UBERON:0002385	34.22	gold quality
gall bladder	UBERON:0002110	33.24	gold quality
rectum	UBERON:0001052	32.79	gold quality
placenta	UBERON:0001987	32.24	gold quality
urinary bladder	UBERON:0001255	31.22	gold quality
blood	UBERON:0000178	31.08	gold quality
uterine cervix	UBERON:0000002	30.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting TDRD15, 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-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-297	99.40	69.58	1418

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tdrd15	ENSDARG00000014039
rattus_norvegicus	Tdrd15	ENSRNOG00000060052
drosophila_melanogaster	tud	FBGN0003891

Paralogs (6): TDRD1 (ENSG00000095627), TDRD5 (ENSG00000162782), TDRD10 (ENSG00000163239), TDRD6 (ENSG00000180113), TDRKH (ENSG00000182134), TDRD7 (ENSG00000196116)

Protein

Protein identifiers

Tudor domain-containing protein 15 — B5MCY1 (reviewed: B5MCY1)

All UniProt accessions (1): B5MCY1

RefSeq proteins (1): NP_001293066* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002999	Tudor	Domain
IPR035437	SNase_OB-fold_sf	Homologous_superfamily
IPR047450	Tudor_TDRD15_rpt1	Domain
IPR047452	Tudor_TDRD15_rpt2	Domain
IPR047454	Tudor_TDRD15_rpt3	Domain
IPR047455	Tudor_TDRD15_rpt4	Domain
IPR047457	Tudor_TDRD15_rpt7	Domain
IPR047459	Tudor_TDRD15_rpt6	Domain
IPR047460	Tudor_TDRD15_rpt5	Domain
IPR050621	Tudor_domain_containing	Family

Pfam: PF00567

UniProt features (11 total): domain 8, chain 1, compositionally biased region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B5MCY1-F1	72.13	0.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): SRSF9_TARGET_GENES, MIR3671, MIR186_5P, MIR513A_3P_MIR513C_3P, MIR4495, MIR410_3P, MIR3124_3P, MIR676_5P, MIR451B, MIR3674, MIR5007_3P, MIR1304_3P, MIR4752, MIR514A_5P, MIR3146

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

722 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TDRD15	TDRD12	Q587J7	560
TDRD15	PIWIL3	Q7Z3Z3	504
TDRD15	PIWIL1	Q96J94	497
TDRD15	TDRD5	Q8NAT2	496
TDRD15	TDRD9	Q8NDG6	494
TDRD15	RIMBP3B	A6NNM3	481
TDRD15	CFAP73	A6NFT4	463
TDRD15	TDRKH	Q9Y2W6	450
TDRD15	EXD1	Q8NHP7	447
TDRD15	TDRD7	Q8NHU6	444
TDRD15	FAM24B	Q8N5W8	439
TDRD15	STK31	Q9BXU1	432
TDRD15	PRSS37	A4D1T9	430
TDRD15	RIMBP3C	A6NJZ7	419
TDRD15	PIWIL2	Q8TC59	417

IntAct

0 interactions, top by confidence:

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: A0JM98, A1L1H3, A6NAF9, A9CPT4, B4F7C4, B5MCY1, D2H3M0, E1BPH3, E2QTD3, Q1L981, Q5VCS6, Q8NAT2, Q4R3G4, Q9BXT4, Q99MV7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

689 predictions. Top by Δscore:

Variant	Effect	Δscore
2:21130789:T:TA	donor_gain	0.9900
2:21130790:A:AA	donor_gain	0.9900
2:21130791:G:GG	donor_gain	0.9600
2:21134846:GT:G	donor_gain	0.9500
2:21137829:T:TA	donor_gain	0.9500
2:21137830:A:AA	donor_gain	0.9500
2:21124345:GTGT:G	donor_gain	0.9400
2:21124075:T:A	donor_gain	0.9300
2:21124043:CTTGG:C	donor_loss	0.9200
2:21124044:TTGG:T	donor_loss	0.9200
2:21124045:TGG:T	donor_loss	0.9200
2:21124046:GG:G	donor_loss	0.9200
2:21124048:TAAAC:T	donor_loss	0.9200
2:21124049:A:C	donor_loss	0.9200
2:21124296:G:GT	donor_gain	0.9200
2:21130769:C:T	donor_gain	0.9200
2:21124349:G:GG	donor_gain	0.9100
2:21133623:T:G	donor_gain	0.9100
2:21137463:A:AG	acceptor_gain	0.9100
2:21137464:G:GG	acceptor_gain	0.9100
2:21124058:C:G	donor_gain	0.9000
2:21124347:GT:G	donor_gain	0.9000
2:21137464:GAAA:G	acceptor_gain	0.8800
2:21124047:G:GG	donor_gain	0.8700
2:21137831:G:GG	donor_gain	0.8700
2:21134848:G:GG	donor_gain	0.8600
2:21124014:G:T	donor_gain	0.8500
2:21124067:T:G	donor_gain	0.8400
2:21124284:T:G	donor_gain	0.8400
2:21124341:GGCT:G	donor_gain	0.8300

AlphaMissense

12807 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:21138380:T:A	W305R	0.993
2:21138380:T:C	W305R	0.993
2:21137873:T:A	W136R	0.992
2:21137873:T:C	W136R	0.992
2:21139117:A:C	R550S	0.992
2:21139117:A:T	R550S	0.992
2:21139118:G:C	A551P	0.992
2:21140557:A:C	R1030S	0.992
2:21140557:A:T	R1030S	0.992
2:21138388:A:C	R307S	0.991
2:21138388:A:T	R307S	0.991
2:21137701:A:C	R78S	0.988
2:21137701:A:T	R78S	0.988
2:21139086:C:A	A540D	0.988
2:21139119:C:A	A551D	0.988
2:21137693:T:A	W76R	0.987
2:21137693:T:C	W76R	0.987
2:21139116:G:C	R550T	0.984
2:21141818:T:A	W1451R	0.984
2:21141818:T:C	W1451R	0.984
2:21139918:A:C	R817S	0.983
2:21139918:A:T	R817S	0.983
2:21142864:A:C	R1799S	0.983
2:21142864:A:T	R1799S	0.983
2:21139079:T:C	C538R	0.981
2:21139289:T:A	W608R	0.981
2:21139289:T:C	W608R	0.981
2:21141551:G:C	A1362P	0.981
2:21138387:G:C	R307T	0.980
2:21138486:T:A	L340H	0.980

dbSNP variants (sampled 300 via entrez): RS1000178960 (2:21127435 T>G), RS1000509049 (2:21130373 A>G), RS1000600682 (2:21135385 A>G), RS1000871815 (2:21145653 AT>A), RS1001034727 (2:21135571 A>G), RS1001064053 (2:21129180 A>C), RS1001070753 (2:21122906 A>C), RS1001126590 (2:21131876 A>T), RS1001379385 (2:21125383 C>G,T), RS1001410342 (2:21125014 G>A,T), RS1001428787 (2:21138368 C>T), RS1001440173 (2:21123143 G>A), RS1001584806 (2:21141669 T>G), RS1001863532 (2:21128748 T>C), RS1001970214 (2:21143839 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

31 associations (top):

Study	Trait	p-value
GCST008074_88	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	6.000000e-06
GCST008077_3	LDL cholesterol levels	9.000000e-57
GCST008077_33	LDL cholesterol levels	1.000000e-06
GCST008077_39	LDL cholesterol levels	7.000000e-10
GCST008077_43	LDL cholesterol levels	5.000000e-14
GCST008077_49	LDL cholesterol levels	1.000000e-78
GCST008078_135	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2.000000e-193
GCST008078_50	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2.000000e-11
GCST008078_79	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	4.000000e-13
GCST008078_87	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2.000000e-22
GCST008078_98	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	5.000000e-226
GCST008079_105	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	5.000000e-213
GCST008079_32	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2.000000e-249
GCST008079_78	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	6.000000e-11
GCST008079_86	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	1.000000e-14
GCST008079_97	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	3.000000e-23
GCST008086_105	LDL cholesterol levels in current drinkers	2.000000e-127
GCST008086_109	LDL cholesterol levels in current drinkers	2.000000e-18
GCST008086_113	LDL cholesterol levels in current drinkers	2.000000e-101
GCST008086_89	LDL cholesterol levels in current drinkers	1.000000e-10
GCST008086_96	LDL cholesterol levels in current drinkers	9.000000e-10
GCST008087_1	Triglyceride levels in current drinkers	2.000000e-06
GCST010243_118	Apolipoprotein B levels	9.000000e-12
GCST010244_146	Triglyceride levels	2.000000e-12
GCST010245_216	LDL cholesterol levels	2.000000e-103
GCST010480_2	Coronary artery disease	1.000000e-10
GCST010866_31	Coronary artery disease	2.000000e-13
GCST011365_84	Myocardial infarction	4.000000e-07
GCST011679_1	Depression in multiple sclerosis (pre-diagnosis)	2.000000e-06
GCST011683_2	Low density lipoprotein cholesterol levels	7.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004329	alcohol drinking
EFO:0004615	apolipoprotein B measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
perfluorooctane sulfonic acid	decreases expression	1

Clinical trials (associated diseases)

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