TRIM49D1

Summary

TRIM49D1 (tripartite motif containing 49D1, HGNC:43973) is a protein-coding gene on chromosome 11q14.3, encoding Tripartite motif-containing protein 49D (C9J1S8).

Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response and regulation of gene expression. Predicted to be active in cytoplasm.

Source: NCBI Gene 399939 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_001384911

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43973
Approved symbol	TRIM49D1
Name	tripartite motif containing 49D1
Location	11q14.3
Locus type	gene with protein product
Status	Approved
Aliases	TRIM49D
Ensembl gene	ENSG00000223417
Ensembl biotype	protein_coding
Entrez	399939

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000420869, ENST00000530311, ENST00000605881

RefSeq mRNA: 2 — MANE Select: NM_001384911 NM_001206627, NM_001384911

CCDS: CCDS60930

Canonical transcript exons

ENST00000420869 — 8 exons

Exon	Start	End
ENSE00001653603	89911409	89912086
ENSE00001745470	89920299	89920509
ENSE00003506682	89916919	89917014
ENSE00003569330	89914912	89915142
ENSE00003615088	89917300	89917714
ENSE00003615850	89913204	89913301
ENSE00003665630	89914175	89914197
ENSE00003916710	89921852	89922245

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 87.09.

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	87.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.94	gold quality
monocyte	CL:0000576	43.44	gold quality
leukocyte	CL:0000738	42.02	gold quality
ganglionic eminence	UBERON:0004023	37.25	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
bone marrow	UBERON:0002371	34.66	silver quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
duodenum	UBERON:0002114	32.87	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	32.13	gold quality
blood	UBERON:0000178	31.97	silver quality
prefrontal cortex	UBERON:0000451	31.40	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
primary visual cortex	UBERON:0002436	30.76	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
frontal cortex	UBERON:0001870	29.22	silver quality
liver	UBERON:0002107	29.06	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	27.97	silver quality
lymph node	UBERON:0000029	27.57	gold quality
cerebral cortex	UBERON:0000956	27.19	silver quality
tonsil	UBERON:0002372	27.05	gold quality
urinary bladder	UBERON:0001255	26.88	gold quality
superior frontal gyrus	UBERON:0002661	26.88	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.63
E-MTAB-6386	no	29.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting TRIM49D1, 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-188-3P	100.00	68.76	1240
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-4721	99.26	66.05	818
HSA-MIR-6506-5P	99.04	65.66	1386
HSA-MIR-619-5P	98.57	64.97	1988
HSA-MIR-676-3P	97.86	65.70	668
HSA-MIR-10526-3P	97.86	64.97	1342
HSA-MIR-4314	97.50	67.30	1369
HSA-MIR-2355-3P	96.84	68.54	909

Cross-species orthologs

0 orthologs

Paralogs (80): MID2 (ENSG00000080561), TRIM9 (ENSG00000100505), MID1 (ENSG00000101871), MEFV (ENSG00000103313), TRIM35 (ENSG00000104228), TRIM14 (ENSG00000106785), TRIM37 (ENSG00000108395), TRIM2 (ENSG00000109654), TRIM3 (ENSG00000110171), TRIM38 (ENSG00000112343), TRIM62 (ENSG00000116525), TRIM67 (ENSG00000119283), TRIM32 (ENSG00000119401), BSPRY (ENSG00000119411), TRIM25 (ENSG00000121060), TRIM6 (ENSG00000121236), TRIM24 (ENSG00000122779), TRIM51 (ENSG00000124900), TRIM28 (ENSG00000130726), TRIM21 (ENSG00000132109), TRIM5 (ENSG00000132256), TRIM22 (ENSG00000132274), TRIM47 (ENSG00000132481), TRIM45 (ENSG00000134253), TRIM29 (ENSG00000137699), TRIM54 (ENSG00000138100), PML (ENSG00000140464), TRIM65 (ENSG00000141569), TRIM43B (ENSG00000144010), TRIM43 (ENSG00000144015), TRIM7 (ENSG00000146054), TRIM41 (ENSG00000146063), TRIM50 (ENSG00000146755), TRIM4 (ENSG00000146833), TRIM55 (ENSG00000147573), TRIM48 (ENSG00000150244), TRIM36 (ENSG00000152503), TRIM11 (ENSG00000154370), TRIM74 (ENSG00000155428), TRIM42 (ENSG00000155890)

Protein

Protein identifiers

Tripartite motif-containing protein 49D — C9J1S8 (reviewed: C9J1S8)

Alternative names: Tripartite motif-containing protein 49-like protein, Tripartite motif-containing protein 49D1, Tripartite motif-containing protein 49D2

All UniProt accessions (2): A0A087WVN7, C9J1S8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the TRIM/RBCC family.

RefSeq proteins (2): NP_001193556, NP_001371840* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000315	Znf_B-box	Domain
IPR001841	Znf_RING	Domain
IPR001870	B30.2/SPRY	Domain
IPR003877	SPRY_dom	Domain
IPR003879	Butyrophylin_SPRY	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR043136	B30.2/SPRY_sf	Homologous_superfamily
IPR050143	TRIM/RBCC	Family

Pfam: PF00622, PF00643, PF15227

UniProt features (10 total): binding site 4, zinc finger region 2, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9J1S8-F1	85.99	0.65

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 93; 96; 115; 121

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_ACTIVITY, MIR506_3P, MIR124_3P, MIR619_5P, MIR4314, MIR2355_3P, MIR6506_5P, chr11q14, GOBP_BIOLOGICAL_PROCESS_INVOLVED_IN_INTERSPECIES_INTERACTION_BETWEEN_ORGANISMS

GO Biological Process (2): regulation of gene expression (GO:0010468), innate immune response (GO:0045087)

GO Molecular Function (4): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), metal ion binding (GO:0046872)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
regulation of macromolecule biosynthetic process	1
immune response	1
defense response to symbiont	1
transition metal ion binding	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
binding	1
cation binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

176 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRIM49D1	TEX101	Q9BY14	367
TRIM49D1	CLEC2D	Q9UHP7	278
TRIM49D1	SLC45A3	Q96JT2	272
TRIM49D1	HMGXB4	Q9UGU5	249
TRIM49D1	YWHAE	P29360	225
TRIM49D1	STMN2	Q93045	224
TRIM49D1	COMMD6	Q7Z4G1	203
TRIM49D1	MS4A2	Q01362	202
TRIM49D1	FOLH1	Q04609	200
TRIM49D1	CAV2	P51636	199
TRIM49D1	PPP1R14C	Q8TAE6	195
TRIM49D1	MS4A1	P08984	190
TRIM49D1	NAALAD2	Q9Y3Q0	184
TRIM49D1	MAB21L2	Q9Y586	183
TRIM49D1	TNFRSF12A	Q9NP84	180

IntAct

0 interactions, top by confidence:

BioGRID (1): TRIM49D2P (Negative Genetic)

ESM2 similar proteins: A0A3B3IT33, A6NCK2, A6NDI0, A6NGJ6, A6NI03, A6NLI5, C9J1S8, I1YAP6, K7N6K2, P0CI25, P0CI26, P15533, Q0PF16, Q1ACD5, Q1ACD6, Q1ACD7, Q1ACD8, Q2YEM8, Q2YEM9, Q2YEN0, Q2YEN2, Q3ZEE5, Q587N6, Q587N7, Q5BN31, Q5C8T6, Q5C8T8, Q5C8U1, Q5C8U3, Q5C8U4, Q5D7H7, Q5D7H8, Q5D7I0, Q5D7I1, Q5D7I2, Q5D7I3, Q5D7I5, Q5D7I6, Q5D7I9, Q5D7J0

Diamond homologs: A0A3B3IT33, A6NCK2, A6NDI0, A6NGJ6, A6NI03, A6NLI5, B0BLU1, C9J1S8, I1YAP6, O00478, O00481, O15344, O75677, O75678, O75679, O76064, P0CI25, P0CI26, P18892, P19474, P62603, P86448, P86449, Q13410, Q2HJ46, Q3C1V9, Q3TL54, Q4KLN8, Q5EBN2, Q5PQN2, Q5R4I2, Q5R996, Q61510, Q62556, Q6INS5, Q6MFY8, Q6UX41, Q6UXE8, Q6ZWI9, Q7T308

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	TRIM49D1	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

761 predictions. Top by Δscore:

Variant	Effect	Δscore
11:89912082:ATCCA:A	acceptor_gain	1.0000
11:89912083:TCCA:T	acceptor_gain	1.0000
11:89912084:CCA:C	acceptor_gain	1.0000
11:89912084:CCAC:C	acceptor_gain	1.0000
11:89912085:CA:C	acceptor_gain	1.0000
11:89912085:CAC:C	acceptor_gain	1.0000
11:89912085:CACTG:C	acceptor_loss	1.0000
11:89912086:ACTGC:A	acceptor_loss	1.0000
11:89912087:C:CC	acceptor_gain	1.0000
11:89912087:CT:C	acceptor_loss	1.0000
11:89913199:CTTA:C	donor_loss	1.0000
11:89913200:TTA:T	donor_loss	1.0000
11:89913201:TACC:T	donor_loss	1.0000
11:89913202:A:AC	donor_gain	1.0000
11:89913202:A:T	donor_loss	1.0000
11:89913202:AC:A	donor_gain	1.0000
11:89913203:C:CA	donor_loss	1.0000
11:89913203:C:CC	donor_gain	1.0000
11:89913203:CC:C	donor_gain	1.0000
11:89913203:CCT:C	donor_gain	1.0000
11:89913297:CACTC:C	acceptor_gain	1.0000
11:89913299:CTC:C	acceptor_gain	1.0000
11:89913300:TC:T	acceptor_gain	1.0000
11:89913301:CC:C	acceptor_gain	1.0000
11:89913301:CCTGC:C	acceptor_loss	1.0000
11:89913302:C:CC	acceptor_gain	1.0000
11:89913302:CTGC:C	acceptor_loss	1.0000
11:89913303:T:C	acceptor_loss	1.0000
11:89915143:CT:C	acceptor_loss	1.0000
11:89917295:CTTA:C	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001164854 (11:89920771 G>C), RS1001912426 (11:89920855 C>A,T), RS1002914345 (11:89921865 C>T), RS1002940177 (11:89923395 T>C), RS1003025300 (11:89922019 C>G), RS1003319530 (11:89923215 T>G), RS1004617406 (11:89911846 T>C), RS1004741188 (11:89923650 G>A,C,T), RS1006309967 (11:89922361 A>C), RS1007112224 (11:89921793 T>C), RS1007557561 (11:89921578 T>C), RS1008151356 (11:89922671 C>G,T), RS1008532381 (11:89922994 G>A), RS1008534714 (11:89922896 T>C), RS1008598266 (11:89923922 A>G,T)

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

1 associations (top):

Study	Trait	p-value
GCST90002380_103	Basophil percentage of white cells	2.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007992	basophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Copper	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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