TRIM49C

Summary

TRIM49C (tripartite motif containing 49C, HGNC:38877) is a protein-coding gene on chromosome 11q14.3, encoding Tripartite motif-containing protein 49C (P0CI26).

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 642612 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 72 total
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_001195234

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:38877
Approved symbol	TRIM49C
Name	tripartite motif containing 49C
Location	11q14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204449
Ensembl biotype	protein_coding
Entrez	642612

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000448984

RefSeq mRNA: 1 — MANE Select: NM_001195234 NM_001195234

CCDS: CCDS53694

Canonical transcript exons

ENST00000448984 — 8 exons

Exon	Start	End
ENSE00002446019	90032397	90032582
ENSE00002474997	90037749	90037979
ENSE00002477855	90041051	90042025
ENSE00002490172	90038693	90038715
ENSE00002506175	90031106	90031244
ENSE00002516588	90035208	90035622
ENSE00002519551	90039865	90039962
ENSE00002528681	90035888	90035983

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 81.33.

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	81.33	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	44.62	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
skeletal muscle tissue	UBERON:0001134	35.65	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
sural nerve	UBERON:0015488	35.28	gold quality
muscle tissue	UBERON:0002385	32.73	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.80	gold quality
lymph node	UBERON:0000029	28.75	gold quality
liver	UBERON:0002107	28.29	gold quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	28.02	gold quality
tonsil	UBERON:0002372	27.05	gold quality
superior frontal gyrus	UBERON:0002661	26.66	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
leukocyte	CL:0000738	26.27	gold quality
blood	UBERON:0000178	26.23	gold quality
monocyte	CL:0000576	26.14	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
muscle of leg	UBERON:0001383	25.31	gold quality
frontal cortex	UBERON:0001870	25.30	gold quality
calcaneal tendon	UBERON:0003701	24.73	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting TRIM49C, 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-3134	100.00	66.43	777
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-580-5P	99.28	70.94	1776
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-5190	99.15	67.76	1234

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 49C — P0CI26 (reviewed: P0CI26)

Alternative names: Tripartite motif-containing protein 49-like protein 2

All UniProt accessions (1): P0CI26

RefSeq proteins (1): NP_001182163* (*=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 (8 total): binding site 4, zinc finger region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CI26-F1	84.53	0.61

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: 20 (showing top): GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_ACTIVITY, MIR9983_3P, MIR506_3P, MIR124_3P, MIR655_3P, MIR374C_5P, MIR129_5P, MIR1252_3P, MIR580_5P, MIR6783_3P, MIR583, MIR1343_3P

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

228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRIM49C	OR4C16	Q8NGL9	542
TRIM49C	ZNG1C	Q5JTY5	471
TRIM49C	POTEJ	P0CG39	470
TRIM49C	TRIM16L	Q309B1	419
TRIM49C	TRIM54	Q9BYV2	354
TRIM49C	FOLH1	Q04609	353
TRIM49C	TRIM46	Q7Z4K8	327
TRIM49C	C8orf82	Q6P1X6	321
TRIM49C	PGM5	Q15124	304
TRIM49C	GOLGA6L6	A8MZA4	301
TRIM49C	UBL4A	P11441	292
TRIM49C	TRIM9	Q9C026	284
TRIM49C	TRIM45	Q9H8W5	280
TRIM49C	FAM131A	Q6UXB0	273
TRIM49C	NAALAD2	Q9Y3Q0	270

IntAct

10 interactions, top by confidence:

A	B	Type	Score
TRIM49C	CKS1B	psi-mi:“MI:0915”(physical association)	0.560
TRIM49C	LIMS4	psi-mi:“MI:0915”(physical association)	0.560
TRIM49C	MINDY3	psi-mi:“MI:0915”(physical association)	0.560
CKS1B	TRIM49C	psi-mi:“MI:0915”(physical association)	0.000
LIMS4	TRIM49C	psi-mi:“MI:0915”(physical association)	0.000
TRIM49C	MINDY3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): TRIM49C (Two-hybrid), TRIM49C (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), TRIM49C (Negative Genetic), TRIM49C (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

1 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	TRIM49C	ubiquitination

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — STAD.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	12
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

663 predictions. Top by Δscore:

Variant	Effect	Δscore
11:90035981:A:T	donor_gain	1.0000
11:90035981:AAGG:A	donor_loss	1.0000
11:90035982:AG:A	donor_loss	1.0000
11:90035983:GG:G	donor_loss	1.0000
11:90035985:T:A	donor_loss	1.0000
11:90037977:CAGGT:C	donor_loss	1.0000
11:90037979:GGT:G	donor_loss	1.0000
11:90037980:G:A	donor_loss	1.0000
11:90038689:TCAGG:T	acceptor_loss	1.0000
11:90038690:CAGGC:C	acceptor_loss	1.0000
11:90038691:A:AG	acceptor_gain	1.0000
11:90038692:G:A	acceptor_loss	1.0000
11:90038692:G:GG	acceptor_gain	1.0000
11:90038717:T:A	donor_loss	1.0000
11:90039863:A:AC	acceptor_loss	1.0000
11:90039863:A:AG	acceptor_gain	1.0000
11:90039863:AG:A	acceptor_gain	1.0000
11:90039864:G:GT	acceptor_gain	1.0000
11:90039864:GG:G	acceptor_gain	1.0000
11:90039864:GGA:G	acceptor_gain	1.0000
11:90039864:GGAGT:G	acceptor_gain	1.0000
11:90039958:CCGAG:C	donor_gain	1.0000
11:90039959:CGAG:C	donor_gain	1.0000
11:90039959:CGAGG:C	donor_loss	1.0000
11:90039960:GAG:G	donor_gain	1.0000
11:90039960:GAGG:G	donor_gain	1.0000
11:90039961:AG:A	donor_gain	1.0000
11:90039961:AGGTA:A	donor_loss	1.0000
11:90039962:GG:G	donor_gain	1.0000
11:90039962:GGTA:G	donor_loss	1.0000

AlphaMissense

3047 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:90039956:T:C	F285L	0.968
11:90039958:C:A	F285L	0.968
11:90039958:C:G	F285L	0.968
11:90041455:T:C	F422L	0.966
11:90041457:T:A	F422L	0.966
11:90041457:T:G	F422L	0.966
11:90041218:T:A	W343R	0.964
11:90041218:T:C	W343R	0.964
11:90041248:T:A	W353R	0.959
11:90041248:T:C	W353R	0.959
11:90035518:T:C	F103L	0.954
11:90035520:C:A	F103L	0.954
11:90035520:C:G	F103L	0.954
11:90041425:T:C	F412L	0.944
11:90041427:C:A	F412L	0.944
11:90041427:C:G	F412L	0.944
11:90035621:G:C	R137P	0.941
11:90041220:G:C	W343C	0.939
11:90041220:G:T	W343C	0.939
11:90041251:G:C	A354P	0.936
11:90041452:A:C	S421R	0.934
11:90041454:C:A	S421R	0.934
11:90041454:C:G	S421R	0.934
11:90035978:T:A	W168R	0.933
11:90035978:T:C	W168R	0.933
11:90041258:G:A	G356D	0.931
11:90041456:T:C	F422S	0.930
11:90041323:T:C	F378L	0.925
11:90041325:T:A	F378L	0.925
11:90041325:T:G	F378L	0.925

dbSNP variants (sampled 300 via entrez): RS1000304693 (11:90058392 T>C), RS1000366687 (11:90061464 A>C), RS1000376202 (11:90041605 A>T), RS1000440406 (11:90060011 G>T), RS1000978175 (11:90045275 A>C,G), RS1001286231 (11:90044892 G>A), RS1001660175 (11:90061973 C>A,G,T), RS1001740813 (11:90043253 CAT>C), RS1001985179 (11:90062353 A>T), RS1002594433 (11:90066260 T>A), RS1002743772 (11:90047803 C>T), RS1003076142 (11:90065397 C>T), RS1003214064 (11:90032378 G>A), RS1003668323 (11:90068215 G>A), RS1003776993 (11:90052588 C>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

1 associations (top):

Study	Trait	p-value
GCST008513_25	Health literacy	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010104	health literacy measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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