MINDY4B (MINDY family member 4B) - Rat Genome Database

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Gene: MINDY4B (MINDY family member 4B) Homo sapiens
Analyze
Symbol: MINDY4B
Name: MINDY family member 4B
RGD ID: 2306135
HGNC Page HGNC:35475
Description: Predicted to enable K48-linked deubiquitinase activity.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C3orf76; CLRN1; FAM188B2; family with sequence similarity 188 member B2; family with sequence similarity 188, member B2; inactive ubiquitin carboxyl-terminal hydrolase MINDY-4B; Putative UPF0526 protein B; UPF0526 protein B-like
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383150,870,376 - 150,905,439 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3150,870,376 - 150,905,439 (-)EnsemblGRCh38hg38GRCh38
GRCh373150,588,163 - 150,623,226 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363152,071,522 - 152,105,916 (-)NCBINCBI36Build 36hg18NCBI36
Celera3149,001,782 - 149,033,992 (-)NCBICelera
Cytogenetic Map3q25.1NCBI
HuRef3147,962,147 - 147,994,318 (-)NCBIHuRef
CHM1_13150,552,171 - 150,572,669 (-)NCBICHM1_1
T2T-CHM13v2.03153,621,470 - 153,656,526 (-)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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16641997   PMID:20379614   PMID:20717163   PMID:21873635  


Genomics

Comparative Map Data
MINDY4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383150,870,376 - 150,905,439 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3150,870,376 - 150,905,439 (-)EnsemblGRCh38hg38GRCh38
GRCh373150,588,163 - 150,623,226 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363152,071,522 - 152,105,916 (-)NCBINCBI36Build 36hg18NCBI36
Celera3149,001,782 - 149,033,992 (-)NCBICelera
Cytogenetic Map3q25.1NCBI
HuRef3147,962,147 - 147,994,318 (-)NCBIHuRef
CHM1_13150,552,171 - 150,572,669 (-)NCBICHM1_1
T2T-CHM13v2.03153,621,470 - 153,656,526 (-)NCBIT2T-CHM13v2.0
Mindy4b-ps
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39358,697,538 - 58,727,655 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl358,695,828 - 58,729,732 (-)EnsemblGRCm39 Ensembl
GRCm38358,790,117 - 58,822,225 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl358,788,407 - 58,822,311 (-)EnsemblGRCm38mm10GRCm38
MGSCv37358,592,325 - 58,595,941 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36358,594,042 - 58,624,137 (-)NCBIMGSCv36mm8
Celera358,482,342 - 58,485,961 (-)NCBICelera
Cytogenetic Map3DNCBI
cM Map328.75NCBI
Mindy4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82145,175,510 - 145,208,165 (-)NCBIGRCr8
mRatBN7.22143,026,685 - 143,061,966 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2143,027,285 - 143,058,144 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02149,004,738 - 149,025,388 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2148,993,072 - 149,014,838 (-)NCBIRnor6.0rn6Rnor6.0
Celera2137,467,657 - 137,488,014 (-)NCBICelera
Cytogenetic Map2q26NCBI
MINDY4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22148,769,814 - 148,804,200 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13148,774,544 - 148,808,930 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03147,898,609 - 147,945,757 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13155,471,591 - 155,491,583 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3155,471,591 - 155,505,966 (-)Ensemblpanpan1.1panPan2
MINDY4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12345,455,973 - 45,481,556 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2345,456,036 - 45,491,057 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2345,322,828 - 45,357,592 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02346,084,496 - 46,119,465 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2346,084,514 - 46,119,471 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12345,673,747 - 45,708,821 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02345,726,308 - 45,761,390 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02346,002,728 - 46,037,458 (-)NCBIUU_Cfam_GSD_1.0
Mindy4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560290,535,159 - 90,564,704 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049367581,203,803 - 1,224,340 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MINDY4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11539,786,459 - 39,825,111 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604112,607,527 - 12,644,022 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mindy4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473028,311,989 - 28,328,865 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q22.3-29(chr3:137126982-198110178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|See cases [RCV000051723] Chr3:137126982..198110178 [GRCh38]
Chr3:136845824..197837049 [GRCh37]
Chr3:138328514..199321446 [NCBI36]
Chr3:3q22.3-29		 pathogenic
GRCh38/hg38 3q24-26.32(chr3:147442566-178522531)x3 copy number gain See cases [RCV000051724] Chr3:147442566..178522531 [GRCh38]
Chr3:147160353..178240319 [GRCh37]
Chr3:148643043..179723013 [NCBI36]
Chr3:3q24-26.32		 pathogenic
GRCh38/hg38 3q24-29(chr3:147521892-198096565)x3 copy number gain See cases [RCV000051725] Chr3:147521892..198096565 [GRCh38]
Chr3:147239679..197823436 [GRCh37]
Chr3:148722369..199307833 [NCBI36]
Chr3:3q24-29		 pathogenic
GRCh38/hg38 3q25.1(chr3:150462960-150915627)x1 copy number loss See cases [RCV000053994] Chr3:150462960..150915627 [GRCh38]
Chr3:150180747..150633414 [GRCh37]
Chr3:151663437..152116104 [NCBI36]
Chr3:3q25.1		 uncertain significance
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q25.1(chr3:150889603-151142420)x3 copy number gain See cases [RCV000138618] Chr3:150889603..151142420 [GRCh38]
Chr3:150607390..150860207 [GRCh37]
Chr3:152090080..152342897 [NCBI36]
Chr3:3q25.1		 likely benign
GRCh37/hg19 3q24-29(chr3:142995020-192997215)x4 copy number gain See cases [RCV000240256] Chr3:142995020..192997215 [GRCh37]
Chr3:3q24-29		 pathogenic
GRCh37/hg19 3q24-25.2(chr3:148425748-153220169)x1 copy number loss See cases [RCV000447056] Chr3:148425748..153220169 [GRCh37]
Chr3:3q24-25.2		 pathogenic
GRCh37/hg19 3q24-26.2(chr3:147180945-168415875)x1 copy number loss See cases [RCV000448130] Chr3:147180945..168415875 [GRCh37]
Chr3:3q24-26.2		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3q25.1-25.2(chr3:150352753-153522663)x1 copy number loss See cases [RCV000510834] Chr3:150352753..153522663 [GRCh37]
Chr3:3q25.1-25.2		 likely pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3q25.1-25.2(chr3:149404255-152786331)x1 copy number loss not provided [RCV001005477] Chr3:149404255..152786331 [GRCh37]
Chr3:3q25.1-25.2		 pathogenic
GRCh37/hg19 3q25.1(chr3:150534295-151213925)x3 copy number gain not provided [RCV001005478] Chr3:150534295..151213925 [GRCh37]
Chr3:3q25.1		 uncertain significance
GRCh37/hg19 3q25.1(chr3:150546825-150878912)x4 copy number gain not provided [RCV002473467] Chr3:150546825..150878912 [GRCh37]
Chr3:3q25.1		 uncertain significance
GRCh37/hg19 3q13.31-26.31(chr3:116620308-172042292)x3 copy number gain not provided [RCV002472621] Chr3:116620308..172042292 [GRCh37]
Chr3:3q13.31-26.31		 pathogenic
GRCh37/hg19 3q25.1(chr3:150534296-150908849)x3 copy number gain not provided [RCV002473873] Chr3:150534296..150908849 [GRCh37]
Chr3:3q25.1		 uncertain significance
GRCh37/hg19 3q22.3-26.1(chr3:138145289-162275610)x3 copy number gain See cases [RCV001194586] Chr3:138145289..162275610 [GRCh37]
Chr3:3q22.3-26.1		 pathogenic
GRCh37/hg19 3q22.3-26.1(chr3:138173683-162494699) copy number gain Global developmental delay [RCV001352648] Chr3:138173683..162494699 [GRCh37]
Chr3:3q22.3-26.1		 pathogenic
GRCh37/hg19 3q24-26.1(chr3:143439359-165252122)x1 copy number loss not provided [RCV001795847] Chr3:143439359..165252122 [GRCh37]
Chr3:3q24-26.1		 pathogenic
GRCh37/hg19 3q23-25.32(chr3:142729607-157921084)x3 copy number gain Brachycephaly [RCV001801182] Chr3:142729607..157921084 [GRCh37]
Chr3:3q23-25.32		 pathogenic
GRCh37/hg19 3q24-25.33(chr3:145486960-160504834) copy number gain not specified [RCV002053375] Chr3:145486960..160504834 [GRCh37]
Chr3:3q24-25.33		 pathogenic
NC_000003.11:g.(?_148447967)_(151176497_?)del deletion Glycogen storage disease XV [RCV003120787] Chr3:148447967..151176497 [GRCh37]
Chr3:3q24-25.1		 pathogenic
Single allele duplication not provided [RCV003448680] Chr3:140154329..197847235 [GRCh37]
Chr3:3q23-29		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:334
Count of miRNA genes:164
Interacting mature miRNAs:167
Transcripts:ENST00000397891, ENST00000465419
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.

Markers in Region
SHGC-80096  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373150,622,045 - 150,622,320UniSTSGRCh37
Build 363152,104,735 - 152,105,010RGDNCBI36
Celera3149,034,993 - 149,035,268RGD
Cytogenetic Map3q25.1UniSTS
HuRef3147,995,319 - 147,995,594UniSTS
TNG Radiation Hybrid Map385956.0UniSTS
D3S3413  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373150,617,102 - 150,617,280UniSTSGRCh37
Build 363152,099,792 - 152,099,970RGDNCBI36
Celera3149,030,050 - 149,030,228RGD
Cytogenetic Map3q25.1UniSTS
HuRef3147,990,428 - 147,990,606UniSTS
Whitehead-RH Map3684.2UniSTS
Whitehead-YAC Contig Map3 UniSTS
NCBI RH Map31321.6UniSTS
D3S3968  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373150,606,163 - 150,606,367UniSTSGRCh37
Build 363152,088,853 - 152,089,057RGDNCBI36
Celera3149,019,110 - 149,019,314RGD
Cytogenetic Map3q25.1UniSTS
HuRef3147,979,486 - 147,979,690UniSTS
Whitehead-RH Map3684.2UniSTS
Whitehead-YAC Contig Map3 UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 1 4 2
Low 10 255 169 20 269 20 12 3 576 16 172 35 3 2 1
Below cutoff 770 1152 776 273 635 219 1894 549 1820 189 981 548 58 430 1228 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000465419   ⟹   ENSP00000491923
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3150,870,376 - 150,905,439 (-)Ensembl
RefSeq Acc Id: ENST00000474598
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3150,901,154 - 150,903,394 (-)Ensembl
RefSeq Acc Id: NM_001351281   ⟹   NP_001338210
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383150,870,376 - 150,905,439 (-)NCBI
T2T-CHM13v2.03153,621,470 - 153,656,526 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001338210 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A8MYZ0 (Get FASTA)   NCBI Sequence Viewer  
  ADO22187 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000491923
  ENSP00000491923.1
Reference Protein Sequences
RefSeq Acc Id: NP_001338210   ⟸   NM_001351281
- UniProtKB: A8MYZ0 (UniProtKB/Swiss-Prot),   A0A1W2PQ44 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000491923   ⟸   ENST00000465419

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A8MYZ0-F1-model_v2 AlphaFold A8MYZ0 1-460 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:35475 AgrOrtholog
COSMIC MINDY4B COSMIC
Ensembl Genes ENSG00000214237 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000465419 ENTREZGENE
  ENST00000465419.7 UniProtKB/Swiss-Prot
GTEx ENSG00000214237 GTEx
HGNC ID HGNC:35475 ENTREZGENE
Human Proteome Map MINDY4B Human Proteome Map
InterPro DUF4205 UniProtKB/Swiss-Prot
  MINY3/4 UniProtKB/Swiss-Prot
NCBI Gene 646951 ENTREZGENE
PANTHER INACTIVE UBIQUITIN CARBOXYL-TERMINAL HYDROLASE MINDY-4B UniProtKB/Swiss-Prot
  PTHR12473 UniProtKB/Swiss-Prot
Pfam DUF4205 UniProtKB/Swiss-Prot
PharmGKB PA165697258 PharmGKB
SMART DUF4205 UniProtKB/Swiss-Prot
UniProt A0A1W2PQ44 ENTREZGENE
  A8MYZ0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A0A1W2PQ44 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-07 MINDY4B  MINDY family member 4B  FAM188B2  family with sequence similarity 188 member B2  Symbol and/or name change 5135510 APPROVED
2015-11-24 FAM188B2  family with sequence similarity 188 member B2    family with sequence similarity 188, member B2  Symbol and/or name change 5135510 APPROVED