TRIM48 (tripartite motif containing 48) - Rat Genome Database

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Gene: TRIM48 (tripartite motif containing 48) Homo sapiens
Analyze
Symbol: TRIM48
Name: tripartite motif containing 48
RGD ID: 1343096
HGNC Page HGNC:19021
Description: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response and regulation of gene expression. Located in cytosol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: E3 ubiquitin-protein ligase TRIM48; MGC4827; RING finger protein 101; RNF101; tripartite motif-containing 48; tripartite motif-containing protein 48
RGD Orthologs
Green Monkey
Alliance Orthologs
More Info more info ...
Related Pseudogenes: LOC100420446   LOC100420449  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381155,262,155 - 55,271,114 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1155,262,155 - 55,271,114 (+)EnsemblGRCh38hg38GRCh38
GRCh371155,029,631 - 55,038,590 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361154,786,234 - 54,795,171 (+)NCBINCBI36Build 36hg18NCBI36
Build 341154,786,233 - 54,795,170NCBI
Celera1152,373,082 - 52,382,021 (+)NCBICelera
Cytogenetic Map11q11NCBI
HuRef1151,358,581 - 51,367,520 (+)NCBIHuRef
T2T-CHM13v2.01155,199,727 - 55,208,688 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IEA)
cytosol  (IDA,IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:21873635   PMID:29186683   PMID:32296183  


Genomics

Comparative Map Data
TRIM48
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381155,262,155 - 55,271,114 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1155,262,155 - 55,271,114 (+)EnsemblGRCh38hg38GRCh38
GRCh371155,029,631 - 55,038,590 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361154,786,234 - 54,795,171 (+)NCBINCBI36Build 36hg18NCBI36
Build 341154,786,233 - 54,795,170NCBI
Celera1152,373,082 - 52,382,021 (+)NCBICelera
Cytogenetic Map11q11NCBI
HuRef1151,358,581 - 51,367,520 (+)NCBIHuRef
T2T-CHM13v2.01155,199,727 - 55,208,688 (+)NCBIT2T-CHM13v2.0
TRIM48
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_0236663031,150 - 6,442 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in TRIM48
32 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_024114.3(TRIM48):c.316G>A (p.Glu106Lys) single nucleotide variant Malignant melanoma [RCV000069441] Chr11:55265171 [GRCh38]
Chr11:55032647 [GRCh37]
Chr11:54789223 [NCBI36]
Chr11:11q11		 not provided
NM_024114.3(TRIM48):c.659G>A (p.Arg220Lys) single nucleotide variant Malignant melanoma [RCV000069442] Chr11:55269322 [GRCh38]
Chr11:55036798 [GRCh37]
Chr11:54793374 [NCBI36]
Chr11:11q11		 not provided
GRCh38/hg38 11q11-12.1(chr11:55265785-56230226)x3 copy number gain See cases [RCV000134403] Chr11:55265785..56230226 [GRCh38]
Chr11:55033261..55997702 [GRCh37]
Chr11:54789837..55754278 [NCBI36]
Chr11:11q11-12.1		 benign
GRCh37/hg19 11q11-12.1(chr11:55033164-55980347)x3 copy number gain See cases [RCV000448938] Chr11:55033164..55980347 [GRCh37]
Chr11:11q11-12.1		 benign
GRCh37/hg19 11q11-12.1(chr11:55029738-55980347)x3 copy number gain See cases [RCV000448359] Chr11:55029738..55980347 [GRCh37]
Chr11:11q11-12.1		 benign
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
NM_024114.5(TRIM48):c.533C>T (p.Thr178Ile) single nucleotide variant not specified [RCV004317465] Chr11:55265673 [GRCh38]
Chr11:55033149 [GRCh37]
Chr11:11q11		 uncertain significance
GRCh37/hg19 11p11.12-q12.1(chr11:51183548-56977098)x3 copy number gain See cases [RCV000512524] Chr11:51183548..56977098 [GRCh37]
Chr11:11p11.12-q12.1		 uncertain significance
GRCh37/hg19 11p11.12-q12.1(chr11:49313405-59008426)x3 copy number gain not provided [RCV000683370] Chr11:49313405..59008426 [GRCh37]
Chr11:11p11.12-q12.1		 uncertain significance
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q11(chr11:54697347-55141349)x3 copy number gain not provided [RCV000737527] Chr11:54697347..55141349 [GRCh37]
Chr11:11q11		 benign
GRCh37/hg19 11q11-12.1(chr11:54697347-56021284)x3 copy number gain not provided [RCV000737528] Chr11:54697347..56021284 [GRCh37]
Chr11:11q11-12.1		 benign
GRCh37/hg19 11q11(chr11:54794237-55134153)x3 copy number gain not provided [RCV000737529] Chr11:54794237..55134153 [GRCh37]
Chr11:11q11		 benign
GRCh37/hg19 11q11-12.1(chr11:54794237-56003589)x3 copy number gain not provided [RCV000737530] Chr11:54794237..56003589 [GRCh37]
Chr11:11q11-12.1		 benign
GRCh37/hg19 11q11(chr11:54892971-55141349)x3 copy number gain not provided [RCV000737531] Chr11:54892971..55141349 [GRCh37]
Chr11:11q11		 benign
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
Single allele duplication not provided [RCV000844966] Chr11:55033164..57518726 [GRCh37]
Chr11:11q11-12.1		 not provided
NM_024114.5(TRIM48):c.635G>C (p.Gly212Ala) single nucleotide variant not specified [RCV004311274] Chr11:55269298 [GRCh38]
Chr11:55036774 [GRCh37]
Chr11:11q11		 uncertain significance
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
NM_024114.5(TRIM48):c.274C>A (p.Leu92Ile) single nucleotide variant not specified [RCV004684715] Chr11:55265129 [GRCh38]
Chr11:55032605 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.446C>T (p.Ala149Val) single nucleotide variant not specified [RCV004684717] Chr11:55265301 [GRCh38]
Chr11:55032777 [GRCh37]
Chr11:11q11		 uncertain significance
GRCh37/hg19 11p11.12-q12.1(chr11:51164494-56879839)x3 copy number gain not provided [RCV001827812] Chr11:51164494..56879839 [GRCh37]
Chr11:11p11.12-q12.1		 uncertain significance
GRCh37/hg19 11p13-q25(chr11:32799481-134938470)x3 copy number gain MISSED ABORTION [RCV002282973] Chr11:32799481..134938470 [GRCh37]
Chr11:11p13-q25		 pathogenic
GRCh37/hg19 11p11.2-q12.2(chr11:51581311-54891247)x3 copy number gain See cases [RCV002286338] Chr11:51581311..54891247 [GRCh37]
Chr11:11p11.2-q12.2		 pathogenic
NM_024114.5(TRIM48):c.202T>C (p.Cys68Arg) single nucleotide variant not specified [RCV004318127] Chr11:55265057 [GRCh38]
Chr11:55032533 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.331A>G (p.Ile111Val) single nucleotide variant not specified [RCV004212880] Chr11:55265186 [GRCh38]
Chr11:55032662 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.137G>A (p.Cys46Tyr) single nucleotide variant not specified [RCV004129916] Chr11:55264992 [GRCh38]
Chr11:55032468 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.56C>A (p.Ser19Tyr) single nucleotide variant not specified [RCV004116001] Chr11:55264911 [GRCh38]
Chr11:55032387 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.497A>C (p.Lys166Thr) single nucleotide variant not specified [RCV004168232] Chr11:55265637 [GRCh38]
Chr11:55033113 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.187C>A (p.Pro63Thr) single nucleotide variant not specified [RCV004149494] Chr11:55265042 [GRCh38]
Chr11:55032518 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.20T>C (p.Val7Ala) single nucleotide variant not specified [RCV004161190] Chr11:55262287 [GRCh38]
Chr11:55029763 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.657C>A (p.Asp219Glu) single nucleotide variant not specified [RCV004122287] Chr11:55269320 [GRCh38]
Chr11:55036796 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.147C>G (p.Ser49Arg) single nucleotide variant not specified [RCV004198448] Chr11:55265002 [GRCh38]
Chr11:55032478 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.8G>A (p.Arg3Gln) single nucleotide variant not specified [RCV004181295] Chr11:55262275 [GRCh38]
Chr11:55029751 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.485C>G (p.Ser162Cys) single nucleotide variant not specified [RCV004193526] Chr11:55265625 [GRCh38]
Chr11:55033101 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.535A>C (p.Thr179Pro) single nucleotide variant not specified [RCV004147956] Chr11:55265675 [GRCh38]
Chr11:55033151 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.667C>A (p.Gln223Lys) single nucleotide variant not specified [RCV004278988] Chr11:55269330 [GRCh38]
Chr11:55036806 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.262A>C (p.Lys88Gln) single nucleotide variant not specified [RCV004271886] Chr11:55265117 [GRCh38]
Chr11:55032593 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.20T>A (p.Val7Glu) single nucleotide variant not specified [RCV004248620] Chr11:55262287 [GRCh38]
Chr11:55029763 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.631G>A (p.Ala211Thr) single nucleotide variant not specified [RCV004253838] Chr11:55269294 [GRCh38]
Chr11:55036770 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.300A>G (p.Leu100=) single nucleotide variant not provided [RCV003390055] Chr11:55265155 [GRCh38]
Chr11:55032631 [GRCh37]
Chr11:11q11		 likely benign
GRCh37/hg19 11p11.12-q13.1(chr11:50398499-63924462)x3 copy number gain not specified [RCV003986918] Chr11:50398499..63924462 [GRCh37]
Chr11:11p11.12-q13.1		 likely pathogenic
NM_024114.5(TRIM48):c.632C>T (p.Ala211Val) single nucleotide variant not specified [RCV004475918] Chr11:55269295 [GRCh38]
Chr11:55036771 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.124G>T (p.Val42Phe) single nucleotide variant not specified [RCV004475913] Chr11:55264979 [GRCh38]
Chr11:55032455 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.622G>A (p.Ala208Thr) single nucleotide variant not specified [RCV004475917] Chr11:55269285 [GRCh38]
Chr11:55036761 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.260A>C (p.Lys87Thr) single nucleotide variant not specified [RCV004475915] Chr11:55265115 [GRCh38]
Chr11:55032591 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.14T>A (p.Ile5Asn) single nucleotide variant not specified [RCV004475914] Chr11:55262281 [GRCh38]
Chr11:55029757 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.98T>C (p.Ile33Thr) single nucleotide variant not specified [RCV004475919] Chr11:55264953 [GRCh38]
Chr11:55032429 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.292C>A (p.Leu98Ile) single nucleotide variant not specified [RCV004475916] Chr11:55265147 [GRCh38]
Chr11:55032623 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.26C>A (p.Thr9Asn) single nucleotide variant not specified [RCV004687662] Chr11:55262293 [GRCh38]
Chr11:55029769 [GRCh37]
Chr11:11q11		 uncertain significance
NM_024114.5(TRIM48):c.154A>G (p.Arg52Gly) single nucleotide variant not specified [RCV004687663] Chr11:55265009 [GRCh38]
Chr11:55032485 [GRCh37]
Chr11:11q11		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:261
Count of miRNA genes:237
Interacting mature miRNAs:248
Transcripts:ENST00000417545
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
20 75 443 148 703 24 70 9 88 8 579 336 291 6 153 20 128 56 1

Sequence


Ensembl Acc Id: ENST00000417545   ⟹   ENSP00000402414
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1155,262,155 - 55,271,114 (+)Ensembl
RefSeq Acc Id: NM_024114   ⟹   NP_077019
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381155,262,155 - 55,271,114 (+)NCBI
GRCh371155,029,658 - 55,038,595 (+)RGD
Build 361154,786,234 - 54,795,171 (+)NCBI Archive
Celera1152,373,082 - 52,382,021 (+)RGD
HuRef1151,358,581 - 51,367,520 (+)RGD
T2T-CHM13v2.01155,199,727 - 55,208,688 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_077019 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH01862 (Get FASTA)   NCBI Sequence Viewer  
  AAO14946 (Get FASTA)   NCBI Sequence Viewer  
  EAW73670 (Get FASTA)   NCBI Sequence Viewer  
  EAW73671 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000402414
  ENSP00000402414.2
GenBank Protein Q8IWZ4 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_077019   ⟸   NM_024114
- UniProtKB: Q9BUW4 (UniProtKB/Swiss-Prot),   Q8IWZ4 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000402414   ⟸   ENST00000417545

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8IWZ4-F1-model_v2 AlphaFold Q8IWZ4 1-224 view protein structure

Promoters
RGD ID:7220297
Promoter ID:EPDNEW_H15894
Type:multiple initiation site
Name:TRIM48_1
Description:tripartite motif containing 48
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381155,262,155 - 55,262,215EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:19021 AgrOrtholog
COSMIC TRIM48 COSMIC
Ensembl Genes ENSG00000150244 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000417545 ENTREZGENE
  ENST00000417545.5 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot
  Classic Zinc Finger UniProtKB/Swiss-Prot
GTEx ENSG00000150244 GTEx
HGNC ID HGNC:19021 ENTREZGENE
Human Proteome Map TRIM48 Human Proteome Map
InterPro TRIM/RBCC UniProtKB/Swiss-Prot
  Znf_B-box UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
KEGG Report hsa:79097 UniProtKB/Swiss-Prot
NCBI Gene 79097 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM UniProtKB/Swiss-Prot
  TRIPARTITE MOTIF-CONTAINING PROTEIN 48 UniProtKB/Swiss-Prot
Pfam zf-B_box UniProtKB/Swiss-Prot
  zf-C3HC4_4 UniProtKB/Swiss-Prot
PharmGKB PA134981425 PharmGKB
PROSITE ZF_BBOX UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
SMART BBOX UniProtKB/Swiss-Prot
  RING UniProtKB/Swiss-Prot
Superfamily-SCOP B-box zinc-binding domain UniProtKB/Swiss-Prot
  RING/U-box UniProtKB/Swiss-Prot
UniProt Q8IWZ4 ENTREZGENE
  Q9BUW4 ENTREZGENE
  TRI48_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary Q9BUW4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-27 TRIM48  tripartite motif containing 48  TRIM48  tripartite motif-containing 48  Symbol and/or name change 5135510 APPROVED