ST20-MTHFS (ST20-MTHFS readthrough) - Rat Genome Database

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Gene: ST20-MTHFS (ST20-MTHFS readthrough) Homo sapiens
Analyze
Symbol: ST20-MTHFS
Name: ST20-MTHFS readthrough
RGD ID: 7205260
HGNC Page HGNC
Description: Predicted to enable 5-formyltetrahydrofolate cyclo-ligase activity; ATP binding activity; and metal ion binding activity.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 5,10-methenyl-tetrahydrofolate synthetase; 5-formyltetrahydrofolate cyclo-ligase; Methenyl-THF synthetase; MTHFS
RGD Orthologs
Mouse
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
GRCh38.p13 Ensembl1579,845,150 - 79,923,754 (-)EnsemblGRCh38hg38GRCh38
GRCh381579,843,547 - 79,923,092 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371580,135,889 - 80,215,434 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map15q25.1NCBI
HuRef1556,894,007 - 56,973,471 (-)NCBIHuRef
CHM1_11580,252,880 - 80,332,383 (-)NCBICHM1_1
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

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Colon cancer  (IAGP)
References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24024966  


Genomics

Comparative Map Data
ST20-MTHFS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1579,845,150 - 79,923,754 (-)EnsemblGRCh38hg38GRCh38
GRCh381579,843,547 - 79,923,092 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371580,135,889 - 80,215,434 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map15q25.1NCBI
HuRef1556,894,007 - 56,973,471 (-)NCBIHuRef
CHM1_11580,252,880 - 80,332,383 (-)NCBICHM1_1
Mthfsl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39988,567,683 - 88,602,373 (-)NCBIGRCm39mm39
GRCm39 Ensembl988,570,655 - 88,602,349 (-)Ensembl
GRCm38988,685,630 - 88,720,320 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl988,688,602 - 88,720,296 (-)EnsemblGRCm38mm10GRCm38
MGSCv37988,583,443 - 88,614,636 (-)NCBIGRCm37mm9NCBIm37
MGSCv36988,577,770 - 88,614,651 (-)NCBImm8
Celera987,285,814 - 87,287,436 (+)NCBICelera
Cytogenetic Map9E3.1NCBI

Position Markers
WI-20294  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371580,137,320 - 80,137,618UniSTSGRCh37
Build 361577,924,375 - 77,924,673RGDNCBI36
Celera1557,073,630 - 57,073,928RGD
Cytogenetic Map15q25.1UniSTS
HuRef1556,895,438 - 56,895,736UniSTS
GeneMap99-GB4 RH Map15277.54UniSTS
Whitehead-RH Map15301.9UniSTS
NCBI RH Map15528.8UniSTS
RH78912  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371580,137,331 - 80,137,496UniSTSGRCh37
Build 361577,924,386 - 77,924,551RGDNCBI36
Celera1557,073,641 - 57,073,806RGD
Cytogenetic Map15q25.1UniSTS
HuRef1556,895,449 - 56,895,614UniSTS
GeneMap99-GB4 RH Map15280.77UniSTS
NCBI RH Map15528.8UniSTS
RH77833  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371580,135,965 - 80,136,207UniSTSGRCh37
Build 361577,923,020 - 77,923,262RGDNCBI36
Celera1557,072,275 - 57,072,517RGD
Cytogenetic Map15q25.1UniSTS
HuRef1556,894,083 - 56,894,325UniSTS
GeneMap99-GB4 RH Map15278.06UniSTS
NCBI RH Map15528.8UniSTS
RH17648  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371580,137,546 - 80,137,676UniSTSGRCh37
Build 361577,924,601 - 77,924,731RGDNCBI36
Celera1557,073,856 - 57,073,986RGD
Cytogenetic Map15q25.1UniSTS
HuRef1556,895,664 - 56,895,794UniSTS
GeneMap99-GB4 RH Map15276.09UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:231
Count of miRNA genes:223
Interacting mature miRNAs:230
Transcripts:ENST00000479961, ENST00000494999
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
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 visual system appendage entire extraembryonic component pharyngeal arch
High
Medium 6 3 1 4 1 2 11 1 1 4 1 1 1
Low 99 16 89 65 208 68 147 54 113 70 155 229 10 4 1
Below cutoff 73 3 134 95 171 95 140 8 28 176 108 128 1 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000479961   ⟹   ENSP00000455643
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1579,845,195 - 79,923,744 (-)Ensembl
RefSeq Acc Id: ENST00000494999   ⟹   ENSP00000489298
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1579,845,376 - 79,923,754 (-)Ensembl
RefSeq Acc Id: ENST00000615374   ⟹   ENSP00000489525
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1579,845,150 - 79,923,106 (-)Ensembl
RefSeq Acc Id: NM_001199760   ⟹   NP_001186689
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381579,843,547 - 79,923,092 (-)NCBI
GRCh371580,135,889 - 80,215,448 (-)NCBI
HuRef1556,894,007 - 56,973,471 (-)NCBI
CHM1_11580,252,880 - 80,332,383 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001186689 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001186689   ⟸   NM_001199760
- UniProtKB: A0A0A6YYL1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000455643   ⟸   ENST00000479961
RefSeq Acc Id: ENSP00000489298   ⟸   ENST00000494999
RefSeq Acc Id: ENSP00000489525   ⟸   ENST00000615374


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 15q24.2-26.3(chr15:75307767-101723215)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052346]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052346]|See cases [RCV000052346] Chr15:75307767..101723215 [GRCh38]
Chr15:75600108..102263418 [GRCh37]
Chr15:73387161..100080941 [NCBI36]
Chr15:15q24.2-26.3
pathogenic
GRCh38/hg38 15q24.3-26.3(chr15:77543797-101843411)x3 copy number gain See cases [RCV000052347] Chr15:77543797..101843411 [GRCh38]
Chr15:77836139..102383614 [GRCh37]
Chr15:75623194..100201137 [NCBI36]
Chr15:15q24.3-26.3
pathogenic
GRCh38/hg38 15q25.1(chr15:79552851-80526230)x3 copy number gain See cases [RCV000052107] Chr15:79552851..80526230 [GRCh38]
Chr15:79845193..80818571 [GRCh37]
Chr15:77632248..78605626 [NCBI36]
Chr15:15q25.1
uncertain significance
GRCh38/hg38 15q24.2-25.1(chr15:76006154-79982417)x1 copy number loss See cases [RCV000137079] Chr15:76006154..79982417 [GRCh38]
Chr15:76298495..80274759 [GRCh37]
Chr15:74085550..78061814 [NCBI36]
Chr15:15q24.2-25.1
pathogenic|uncertain significance
GRCh38/hg38 15q23-26.3(chr15:72154949-101920998)x3 copy number gain See cases [RCV000143019] Chr15:72154949..101920998 [GRCh38]
Chr15:72447290..102461201 [GRCh37]
Chr15:70234344..100278724 [NCBI36]
Chr15:15q23-26.3
pathogenic
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3 copy number gain See cases [RCV000142915] Chr15:59828460..101920998 [GRCh38]
Chr15:60120659..102461201 [GRCh37]
Chr15:57907951..100278724 [NCBI36]
Chr15:15q22.2-26.3
pathogenic
GRCh37/hg19 15q24.2-26.3(chr15:76061144-102429112)x3 copy number gain See cases [RCV000511332] Chr15:76061144..102429112 [GRCh37]
Chr15:15q24.2-26.3
pathogenic
GRCh37/hg19 15q22.31-26.3(chr15:64637227-102509910)x3 copy number gain See cases [RCV000240602] Chr15:64637227..102509910 [GRCh37]
Chr15:15q22.31-26.3
pathogenic
NM_001199758.1(MTHFS):c.313C>T (p.Gln105Ter) single nucleotide variant Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination [RCV000766132] Chr15:79845338 [GRCh38]
Chr15:80137680 [GRCh37]
Chr15:15q25.1
pathogenic|likely pathogenic|uncertain significance
GRCh37/hg19 15q22.1-26.3(chr15:59297293-102480888)x3 copy number gain not provided [RCV000415836] Chr15:59297293..102480888 [GRCh37]
Chr15:15q22.1-26.3
likely pathogenic
NM_001199758.1(MTHFS):c.-55+279T>C single nucleotide variant Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination [RCV000766131] Chr15:79896882 [GRCh38]
Chr15:80189224 [GRCh37]
Chr15:15q25.1
pathogenic
GRCh37/hg19 15q15.1-26.3(chr15:41745084-102354798)x4 copy number gain See cases [RCV000447123] Chr15:41745084..102354798 [GRCh37]
Chr15:15q15.1-26.3
pathogenic
GRCh37/hg19 15q25.1(chr15:79755580-80159956)x1 copy number loss See cases [RCV000447185] Chr15:79755580..80159956 [GRCh37]
Chr15:15q25.1
likely benign
GRCh37/hg19 15q11.2-26.3(chr15:20733395-102511616)x4 copy number gain See cases [RCV000447765] Chr15:20733395..102511616 [GRCh37]
Chr15:15q11.2-26.3
pathogenic
GRCh37/hg19 15q11.2-26.3(chr15:22770422-102429112)x3 copy number gain See cases [RCV000510717] Chr15:22770422..102429112 [GRCh37]
Chr15:15q11.2-26.3
pathogenic
GRCh37/hg19 15q11.2-26.3(chr15:22770422-102429112) copy number gain See cases [RCV000512019] Chr15:22770422..102429112 [GRCh37]
Chr15:15q11.2-26.3
pathogenic
NM_001199758.1(MTHFS):c.263G>A (p.Arg88Gln) single nucleotide variant Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination [RCV000766130] Chr15:79845388 [GRCh38]
Chr15:80137730 [GRCh37]
Chr15:15q25.1
pathogenic|likely pathogenic|uncertain significance
Single allele duplication not provided [RCV000677926] Chr15:31115047..102354857 [GRCh37]
Chr15:15q13.2-26.3
pathogenic
GRCh37/hg19 15q25.1-25.3(chr15:79023343-87158823)x1,2 copy number gain not provided [RCV000683712] Chr15:79023343..87158823 [GRCh37]
Chr15:15q25.1-25.3
pathogenic
GRCh37/hg19 15q23-26.3(chr15:71329220-102270758)x3 copy number gain not provided [RCV000683703] Chr15:71329220..102270758 [GRCh37]
Chr15:15q23-26.3
pathogenic
GRCh37/hg19 15q24.3-26.3(chr15:77479244-102429112)x3 copy number gain not provided [RCV000683710] Chr15:77479244..102429112 [GRCh37]
Chr15:15q24.3-26.3
pathogenic
GRCh37/hg19 15q25.1(chr15:80137560-80443036)x3 copy number gain not provided [RCV000738849] Chr15:80137560..80443036 [GRCh37]
Chr15:15q25.1
benign
GRCh37/hg19 15q11.1-26.3(chr15:20016811-102493540)x3 copy number gain not provided [RCV000751155] Chr15:20016811..102493540 [GRCh37]
Chr15:15q11.1-26.3
pathogenic
GRCh37/hg19 15q11.1-26.3(chr15:20071673-102461162)x3 copy number gain not provided [RCV000751156] Chr15:20071673..102461162 [GRCh37]
Chr15:15q11.1-26.3
pathogenic
NM_006441.4(MTHFS):c.420C>T (p.Asp140=) single nucleotide variant not provided [RCV000970285] Chr15:79845402 [GRCh38]
Chr15:80137744 [GRCh37]
Chr15:15q25.1
benign
GRCh37/hg19 15q25.1(chr15:79679772-80383301)x3 copy number gain not provided [RCV001259713] Chr15:79679772..80383301 [GRCh37]
Chr15:15q25.1
uncertain significance
NM_001199760.2(ST20-MTHFS):c.45+8524_45+8525insT insertion not provided [RCV000908824] Chr15:79899104..79899105 [GRCh38]
Chr15:80191446..80191447 [GRCh37]
Chr15:15q25.1
likely benign
NC_000015.9:g.(?_32964879)_(91358519_?)dup duplication Bloom syndrome [RCV001343104]|Familial colorectal cancer [RCV001325176] Chr15:32964879..91358519 [GRCh37]
Chr15:15q13.3-26.1
uncertain significance
NM_006441.4(MTHFS):c.104T>C (p.Val35Ala) single nucleotide variant not provided [RCV001358519] Chr15:79896885 [GRCh38]
Chr15:80189227 [GRCh37]
Chr15:15q25.1
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:44655 AgrOrtholog
COSMIC ST20-MTHFS COSMIC
Ensembl Genes ENSG00000259332 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSP00000455643 UniProtKB/TrEMBL
  ENSP00000489298 UniProtKB/TrEMBL
  ENSP00000489525 ENTREZGENE
Ensembl Transcript ENST00000479961 UniProtKB/TrEMBL
  ENST00000494999 UniProtKB/TrEMBL
  ENST00000615374 ENTREZGENE
Gene3D-CATH 3.40.50.10420 UniProtKB/TrEMBL
GTEx ENSG00000259332 GTEx
HGNC ID HGNC:44655 ENTREZGENE
Human Proteome Map ST20-MTHFS Human Proteome Map
InterPro FTHF_cligase UniProtKB/TrEMBL
  FTHF_cligase-like_sf UniProtKB/TrEMBL
  NagB/RpiA_transferase-like UniProtKB/TrEMBL
KEGG Report hsa:100528021 UniProtKB/TrEMBL
NCBI Gene ST20-MTHFS ENTREZGENE
PANTHER PTHR23407:SF1 UniProtKB/TrEMBL
Pfam 5-FTHF_cyc-lig UniProtKB/TrEMBL
PIRSF FTHF_cligase UniProtKB/TrEMBL
Superfamily-SCOP SSF100950 UniProtKB/TrEMBL
TIGRFAMs MTHFS_bact UniProtKB/TrEMBL
UniProt A0A0A6YYL1 ENTREZGENE, UniProtKB/TrEMBL
  A0A0U1RR23_HUMAN UniProtKB/TrEMBL