MIF4GD-DT (MIF4GD divergent transcript) - Rat Genome Database

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Gene: MIF4GD-DT (MIF4GD divergent transcript) Homo sapiens
Analyze
Symbol: MIF4GD-DT
Name: MIF4GD divergent transcript
RGD ID: 16563810
HGNC Page HGNC:55335
Description: ASSOCIATED WITH Amish Lethal Microcephaly; genetic disease; Thiamine Metabolism Dysfunction Syndrome 4 (Bilateral Striatal Degeneration and Progressive Polyneuropathy Type)
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC022211.2; AC022211.3; LOC100287042; novel transcript, antisense to SLC25A19; uncharacterized LOC100287042
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381775,271,299 - 75,273,895 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1775,271,369 - 75,273,895 (+)EnsemblGRCh38hg38GRCh38
GRCh371773,267,380 - 73,269,976 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17q25.1NCBI
HuRef1768,677,584 - 68,680,185 (+)NCBIHuRef
CHM1_11773,331,977 - 73,334,578 (+)NCBICHM1_1
T2T-CHM13v2.01776,163,385 - 76,165,986 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:22658674   PMID:29507755  


Genomics

Variants

.
Variants in MIF4GD-DT
33 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001126121.2(SLC25A19):c.779G>A (p.Arg260Gln) single nucleotide variant Amish lethal microcephaly [RCV001331197]|not provided [RCV001863237] Chr17:75273635 [GRCh38]
Chr17:73269716 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.775-122_775-121insAATAG insertion not provided [RCV001551640] Chr17:75273760..75273761 [GRCh38]
Chr17:73269841..73269842 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.906G>A (p.Ser302=) single nucleotide variant not provided [RCV000967467] Chr17:75273508 [GRCh38]
Chr17:73269589 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.842T>G (p.Phe281Cys) single nucleotide variant Amish lethal microcephaly [RCV001335105]|SLC25A19-related condition [RCV003908045]|not provided [RCV000732359] Chr17:75273572 [GRCh38]
Chr17:73269653 [GRCh37]
Chr17:17q25.1		 likely benign|conflicting interpretations of pathogenicity|uncertain significance
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
NM_001126121.2(SLC25A19):c.775-1G>C single nucleotide variant Amish lethal microcephaly [RCV000853269] Chr17:75273640 [GRCh38]
Chr17:73269721 [GRCh37]
Chr17:17q25.1		 pathogenic
NM_001126121.2(SLC25A19):c.*200G>A single nucleotide variant Amish lethal microcephaly [RCV000380971]|not provided [RCV001590962] Chr17:75273251 [GRCh38]
Chr17:73269332 [GRCh37]
Chr17:17q25.1		 benign|likely benign|uncertain significance
NM_001126121.2(SLC25A19):c.*384C>T single nucleotide variant Amish lethal microcephaly [RCV001123392] Chr17:75273067 [GRCh38]
Chr17:73269148 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.*437T>G single nucleotide variant Amish lethal microcephaly [RCV000275329] Chr17:75273014 [GRCh38]
Chr17:73269095 [GRCh37]
Chr17:17q25.1		 benign|likely benign
NM_001126121.2(SLC25A19):c.930C>A (p.Phe310Leu) single nucleotide variant Amish lethal microcephaly [RCV000384560] Chr17:75273484 [GRCh38]
Chr17:73269565 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.*2T>C single nucleotide variant Amish lethal microcephaly [RCV000327662]|Progressive demyelinating neuropathy with bilateral striatal necrosis [RCV001807078]|not provided [RCV000676626]|not specified [RCV000118365] Chr17:75273449 [GRCh38]
Chr17:73269530 [GRCh37]
Chr17:17q25.1		 benign|likely benign
NM_001126121.2(SLC25A19):c.819G>A (p.Leu273=) single nucleotide variant Amish lethal microcephaly [RCV000282825]|Progressive demyelinating neuropathy with bilateral striatal necrosis [RCV001807080]|not provided [RCV000676627]|not specified [RCV000118371] Chr17:75273595 [GRCh38]
Chr17:73269676 [GRCh37]
Chr17:17q25.1		 benign|likely benign
NM_001126121.2(SLC25A19):c.918C>T (p.Phe306=) single nucleotide variant not provided [RCV002527287]|not specified [RCV000501844] Chr17:75273496 [GRCh38]
Chr17:73269577 [GRCh37]
Chr17:17q25.1		 likely benign
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
NM_001126121.2(SLC25A19):c.775-131AATAA[3] microsatellite not provided [RCV001637828] Chr17:75273760..75273761 [GRCh38]
Chr17:73269841..73269842 [GRCh37]
Chr17:17q25.1		 benign
NM_001126121.2(SLC25A19):c.*408C>T single nucleotide variant Amish lethal microcephaly [RCV001123391] Chr17:75273043 [GRCh38]
Chr17:73269124 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.*292A>G single nucleotide variant Amish lethal microcephaly [RCV001123394] Chr17:75273159 [GRCh38]
Chr17:73269240 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.*301C>T single nucleotide variant Amish lethal microcephaly [RCV001123393] Chr17:75273150 [GRCh38]
Chr17:73269231 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.*164G>A single nucleotide variant Amish lethal microcephaly [RCV001124497] Chr17:75273287 [GRCh38]
Chr17:73269368 [GRCh37]
Chr17:17q25.1		 benign
NM_001126121.2(SLC25A19):c.*113G>C single nucleotide variant Amish lethal microcephaly [RCV000288974] Chr17:75273338 [GRCh38]
Chr17:73269419 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.789G>C (p.Lys263Asn) single nucleotide variant not specified [RCV000193199] Chr17:75273625 [GRCh38]
Chr17:73269706 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.*96G>C single nucleotide variant Amish lethal microcephaly [RCV001124498]|not provided [RCV001570238] Chr17:75273355 [GRCh38]
Chr17:73269436 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.775-11C>T single nucleotide variant not specified [RCV000601568] Chr17:75273650 [GRCh38]
Chr17:73269731 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.879C>T (p.Ala293=) single nucleotide variant not provided [RCV000933029] Chr17:75273535 [GRCh38]
Chr17:73269616 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.*274C>G single nucleotide variant Amish lethal microcephaly [RCV000333409]|not provided [RCV001636917] Chr17:75273177 [GRCh38]
Chr17:73269258 [GRCh37]
Chr17:17q25.1		 benign|likely benign
NM_001126121.2(SLC25A19):c.797T>G (p.Met266Arg) single nucleotide variant Amish lethal microcephaly [RCV000340152]|SLC25A19-related condition [RCV003930038]|not provided [RCV000838506]|not specified [RCV000388085] Chr17:75273617 [GRCh38]
Chr17:73269698 [GRCh37]
Chr17:17q25.1		 likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001126121.2(SLC25A19):c.910G>A (p.Glu304Lys) single nucleotide variant Progressive demyelinating neuropathy with bilateral striatal necrosis [RCV002264846] Chr17:75273504 [GRCh38]
Chr17:73269585 [GRCh37]
Chr17:17q25.1		 pathogenic
NM_001126121.2(SLC25A19):c.869T>A (p.Leu290Gln) single nucleotide variant Progressive demyelinating neuropathy with bilateral striatal necrosis [RCV002264843] Chr17:75273545 [GRCh38]
Chr17:73269626 [GRCh37]
Chr17:17q25.1		 pathogenic
NM_001126121.2(SLC25A19):c.939G>T (p.Met313Ile) single nucleotide variant not provided [RCV002820701] Chr17:75273475 [GRCh38]
Chr17:73269556 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.838G>A (p.Gly280Ser) single nucleotide variant not provided [RCV002621774] Chr17:75273576 [GRCh38]
Chr17:73269657 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.905C>T (p.Ser302Leu) single nucleotide variant Inborn genetic diseases [RCV002719848] Chr17:75273509 [GRCh38]
Chr17:73269590 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.792C>T (p.Gly264=) single nucleotide variant not provided [RCV003030986] Chr17:75273622 [GRCh38]
Chr17:73269703 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.905C>G (p.Ser302Trp) single nucleotide variant Inborn genetic diseases [RCV002722746] Chr17:75273509 [GRCh38]
Chr17:73269590 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.805G>A (p.Ala269Thr) single nucleotide variant not provided [RCV002603494] Chr17:75273609 [GRCh38]
Chr17:73269690 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.959G>A (p.Arg320His) single nucleotide variant not provided [RCV003070310] Chr17:75273455 [GRCh38]
Chr17:73269536 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001126121.2(SLC25A19):c.775-6C>T single nucleotide variant not provided [RCV003845717] Chr17:75273645 [GRCh38]
Chr17:73269726 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.*4C>T single nucleotide variant SLC25A19-related condition [RCV003942255] Chr17:75273447 [GRCh38]
Chr17:73269528 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001126121.2(SLC25A19):c.890G>T (p.Gly297Val) single nucleotide variant Inborn genetic diseases [RCV004456430] Chr17:75273524 [GRCh38]
Chr17:73269605 [GRCh37]
Chr17:17q25.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:419
Count of miRNA genes:318
Interacting mature miRNAs:331
Transcripts:ENST00000582668, ENST00000585075
Prediction methods:Microtar, 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
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 3 2 6 11 10 9 1
Low 1857 1529 1290 275 1302 138 4017 1543 3006 310 1337 1481 148 923 2537 4
Below cutoff 572 1432 422 338 619 317 336 649 691 107 101 117 21 281 249

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000582668
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1775,271,398 - 75,273,722 (+)Ensembl
RefSeq Acc Id: ENST00000585075
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1775,271,369 - 75,273,895 (+)Ensembl
RefSeq Acc Id: NR_036520
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381775,271,299 - 75,273,895 (+)NCBI
T2T-CHM13v2.01776,163,385 - 76,165,986 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAH12291 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC MIF4GD-DT COSMIC
Ensembl Genes ENSG00000263843 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000585075 ENTREZGENE
GTEx ENSG00000263843 GTEx
HGNC ID HGNC:55335 ENTREZGENE
Human Proteome Map MIF4GD-DT Human Proteome Map
NCBI Gene LOC100287042 ENTREZGENE
RNAcentral URS000075AA2D RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-10-26 MIF4GD-DT  MIF4GD divergent transcript  AC022211.2  novel transcript, antisense to SLC25A19  Symbol and/or name change 19259463 PROVISIONAL
2020-08-20 AC022211.2  novel transcript, antisense to SLC25A19  AC022211.3  novel transcript, antisense to SLC25A19  Symbol and/or name change 19259462 PROVISIONAL
2020-06-25 AC022211.3  novel transcript, antisense to SLC25A19  LOC100287042  uncharacterized LOC100287042  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100287042  uncharacterized LOC100287042  AC022211.3  novel transcript, antisense to SLC25A19  Symbol and/or name change 5135510 APPROVED
2020-02-07 AC022211.3  novel transcript, antisense to SLC25A19  AC022211.2  novel transcript, antisense to SLC25A19  Symbol and/or name change 19259462 PROVISIONAL