TMEM53 (transmembrane protein 53) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: TMEM53 (transmembrane protein 53) Homo sapiens
Analyze
Symbol: TMEM53
Name: transmembrane protein 53
RGD ID: 1603008
HGNC Page HGNC:26186
Description: Involved in negative regulation of BMP signaling pathway; negative regulation of ossification; and regulation of nucleocytoplasmic transport. Located in nuclear membrane. Implicated in craniotubular dysplasia Ikegawa type.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CTDI; FLJ22353; NET4; novel DUF829 domain-containing protein; nuclear envelope transmembrane protein 4; RP4-678E16.2
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38144,653,247 - 44,674,481 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl144,635,238 - 44,674,481 (-)EnsemblGRCh38hg38GRCh38
GRCh37145,118,919 - 45,140,153 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36144,892,088 - 44,912,686 (-)NCBINCBI36Build 36hg18NCBI36
Celera143,402,390 - 43,422,988 (-)NCBICelera
Cytogenetic Map1p34.1NCBI
HuRef143,233,694 - 43,254,292 (-)NCBIHuRef
CHM1_1145,235,410 - 45,256,009 (-)NCBICHM1_1
T2T-CHM13v2.0144,524,186 - 44,545,427 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View
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:8125298   PMID:8889548   PMID:12477932   PMID:12958361   PMID:17207965   PMID:18029348   PMID:21630459   PMID:21832049   PMID:28514442   PMID:29117863   PMID:31056421   PMID:33824347  
PMID:33961781  


Genomics

Comparative Map Data
TMEM53
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38144,653,247 - 44,674,481 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl144,635,238 - 44,674,481 (-)EnsemblGRCh38hg38GRCh38
GRCh37145,118,919 - 45,140,153 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36144,892,088 - 44,912,686 (-)NCBINCBI36Build 36hg18NCBI36
Celera143,402,390 - 43,422,988 (-)NCBICelera
Cytogenetic Map1p34.1NCBI
HuRef143,233,694 - 43,254,292 (-)NCBIHuRef
CHM1_1145,235,410 - 45,256,009 (-)NCBICHM1_1
T2T-CHM13v2.0144,524,186 - 44,545,427 (-)NCBIT2T-CHM13v2.0
Tmem53
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394117,109,148 - 117,125,785 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4117,109,148 - 117,125,779 (+)EnsemblGRCm39 Ensembl
GRCm384117,251,951 - 117,268,588 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4117,251,951 - 117,268,582 (+)EnsemblGRCm38mm10GRCm38
MGSCv374116,924,594 - 116,941,185 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364116,749,921 - 116,766,512 (+)NCBIMGSCv36mm8
Celera4115,981,969 - 115,998,698 (+)NCBICelera
Cytogenetic Map4D1NCBI
cM Map453.43NCBI
Tmem53
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85135,958,344 - 135,974,258 (+)NCBIGRCr8
mRatBN7.25130,721,780 - 130,737,692 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5130,721,659 - 130,737,692 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5133,345,225 - 133,360,784 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05135,099,823 - 135,115,382 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05135,122,252 - 135,137,811 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,112,417 - 136,127,976 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,112,417 - 136,127,976 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05139,905,905 - 139,921,464 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45137,559,894 - 137,575,740 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15137,565,154 - 137,580,579 (+)NCBI
Celera5129,243,073 - 129,258,614 (+)NCBICelera
Cytogenetic Map5q36NCBI
Tmem53
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546413,552,922 - 13,577,528 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546413,552,963 - 13,577,528 (+)NCBIChiLan1.0ChiLan1.0
TMEM53
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21182,134,506 - 182,157,787 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11181,275,852 - 181,299,184 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0143,955,734 - 43,977,107 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1145,322,209 - 45,343,326 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl145,305,359 - 45,343,109 (-)Ensemblpanpan1.1panPan2
TMEM53
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11515,640,232 - 15,661,829 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1515,640,342 - 15,678,994 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1515,760,354 - 15,781,933 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01515,791,873 - 15,813,549 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1515,791,913 - 15,830,728 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11515,592,995 - 15,614,578 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01515,660,073 - 15,681,673 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01515,733,773 - 15,755,366 (+)NCBIUU_Cfam_GSD_1.0
Tmem53
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505860,071,166 - 60,090,112 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647425,896,980 - 25,914,963 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647425,897,032 - 25,914,873 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM53
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6166,645,098 - 166,680,654 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16166,645,103 - 166,664,382 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26154,094,633 - 154,112,799 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM53
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12088,111,228 - 88,131,952 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2088,111,231 - 88,134,124 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603328,790,922 - 28,812,672 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem53
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624906544,485 - 580,001 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624906528,595 - 579,894 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in TMEM53
34 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p34.3-33(chr1:39479787-47688131)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051817]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051817]|See cases [RCV000051817] Chr1:39479787..47688131 [GRCh38]
Chr1:39945459..48153803 [GRCh37]
Chr1:39718046..47926390 [NCBI36]
Chr1:1p34.3-33		 pathogenic
GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3 copy number gain See cases [RCV000051803] Chr1:38222737..45636176 [GRCh38]
Chr1:38688409..46101848 [GRCh37]
Chr1:38460996..45874435 [NCBI36]
Chr1:1p34.3-34.1		 pathogenic
GRCh38/hg38 1p34.2-34.1(chr1:40462415-44668040)x1 copy number loss See cases [RCV000053837] Chr1:40462415..44668040 [GRCh38]
Chr1:40928087..45133712 [GRCh37]
Chr1:40700674..44906299 [NCBI36]
Chr1:1p34.2-34.1		 pathogenic
GRCh38/hg38 1p34.1(chr1:43896056-44867736)x3 copy number gain See cases [RCV000142581] Chr1:43896056..44867736 [GRCh38]
Chr1:44361728..45333408 [GRCh37]
Chr1:44134315..45105995 [NCBI36]
Chr1:1p34.1		 uncertain significance
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12		 likely benign
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NM_024587.4(TMEM53):c.707_715dup (p.Arg238_Arg239insLeuAlaArg) duplication Craniotubular dysplasia, Ikegawa type [RCV003313010] Chr1:44654677..44654678 [GRCh38]
Chr1:45120349..45120350 [GRCh37]
Chr1:1p34.1		 uncertain significance
NC_000001.10:g.(?_33241563)_(46663513_?)dup duplication Charcot-Marie-Tooth disease dominant intermediate C [RCV000708276] Chr1:33241563..46663513 [GRCh37]
Chr1:1p35.1-34.1		 uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1		 uncertain significance
GRCh37/hg19 1p34.1(chr1:44810778-45216633)x3 copy number gain not provided [RCV001005081] Chr1:44810778..45216633 [GRCh37]
Chr1:1p34.1		 uncertain significance
GRCh37/hg19 1p34.1(chr1:44424878-45207102)x1 copy number loss not provided [RCV001005080] Chr1:44424878..45207102 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.219_222dup (p.Val75fs) duplication Craniotubular dysplasia, Ikegawa type [RCV001822871]|TMEM53-related craniotubular dysplasia [RCV001290093] Chr1:44655170..44655171 [GRCh38]
Chr1:45120842..45120843 [GRCh37]
Chr1:1p34.1		 pathogenic
NC_000001.10:g.(?_33241563)_(46663513_?)dup duplication Charcot-Marie-Tooth disease, dominant intermediate C [RCV001308684] Chr1:33241563..46663513 [GRCh37]
Chr1:1p35.1-34.1		 uncertain significance
NM_024587.4(TMEM53):c.62-5_62-3del deletion Craniotubular dysplasia, Ikegawa type [RCV001822872]|TMEM53-related craniotubular dysplasia [RCV001290094] Chr1:44660298..44660300 [GRCh38]
Chr1:45125970..45125972 [GRCh37]
Chr1:1p34.1		 pathogenic
GRCh37/hg19 1p34.1(chr1:44346001-46332161)x3 copy number gain See cases [RCV002246181] Chr1:44346001..46332161 [GRCh37]
Chr1:1p34.1		 uncertain significance
GRCh37/hg19 1p35.1-33(chr1:33285582-47891811) copy number gain not specified [RCV002052781] Chr1:33285582..47891811 [GRCh37]
Chr1:1p35.1-33		 pathogenic
NC_000001.10:g.(?_44257753)_(46663493_?)dup duplication Early infantile epileptic encephalopathy with suppression bursts [RCV003109481] Chr1:44257753..46663493 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.791C>T (p.Thr264Ile) single nucleotide variant not specified [RCV004292841] Chr1:44654602 [GRCh38]
Chr1:45120274 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.544G>A (p.Val182Ile) single nucleotide variant not specified [RCV004139245] Chr1:44654849 [GRCh38]
Chr1:45120521 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.814C>T (p.Arg272Cys) single nucleotide variant not specified [RCV004192821] Chr1:44654579 [GRCh38]
Chr1:45120251 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.728G>A (p.Arg243His) single nucleotide variant not specified [RCV004216535] Chr1:44654665 [GRCh38]
Chr1:45120337 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.712C>T (p.Arg238Cys) single nucleotide variant not specified [RCV004111321] Chr1:44654681 [GRCh38]
Chr1:45120353 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.599A>G (p.Tyr200Cys) single nucleotide variant not specified [RCV004135358] Chr1:44654794 [GRCh38]
Chr1:45120466 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.193G>A (p.Val65Ile) single nucleotide variant not specified [RCV004232135] Chr1:44655200 [GRCh38]
Chr1:45120872 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.131G>T (p.Gly44Val) single nucleotide variant not specified [RCV004178016] Chr1:44660226 [GRCh38]
Chr1:45125898 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.100C>T (p.Arg34Trp) single nucleotide variant not specified [RCV004211669] Chr1:44660257 [GRCh38]
Chr1:45125929 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.545T>G (p.Val182Gly) single nucleotide variant not specified [RCV004147155] Chr1:44654848 [GRCh38]
Chr1:45120520 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.182G>A (p.Arg61Lys) single nucleotide variant not specified [RCV004081229] Chr1:44660175 [GRCh38]
Chr1:45125847 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.169A>G (p.Ile57Val) single nucleotide variant not specified [RCV004322924] Chr1:44660188 [GRCh38]
Chr1:45125860 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.343G>A (p.Gly115Ser) single nucleotide variant not specified [RCV004254637] Chr1:44655050 [GRCh38]
Chr1:45120722 [GRCh37]
Chr1:1p34.1		 uncertain significance
Single allele inversion Bilateral polymicrogyria [RCV003459046] Chr1:33246132..61045156 [GRCh38]
Chr1:1p35.1-31.3		 likely pathogenic
NM_024587.4(TMEM53):c.392G>A (p.Arg131His) single nucleotide variant not specified [RCV004347868] Chr1:44655001 [GRCh38]
Chr1:45120673 [GRCh37]
Chr1:1p34.1		 uncertain significance
GRCh37/hg19 1p34.1(chr1:44810778-45212378)x3 copy number gain not specified [RCV003986806] Chr1:44810778..45212378 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.26C>T (p.Thr9Ile) single nucleotide variant TMEM53-related disorder [RCV003911714] Chr1:44674366 [GRCh38]
Chr1:45140038 [GRCh37]
Chr1:1p34.1		 likely benign
NM_024587.4(TMEM53):c.688C>T (p.Arg230Cys) single nucleotide variant not specified [RCV004470376] Chr1:44654705 [GRCh38]
Chr1:45120377 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.400C>T (p.Arg134Cys) single nucleotide variant not specified [RCV004470372] Chr1:44654993 [GRCh38]
Chr1:45120665 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.625C>T (p.Arg209Cys) single nucleotide variant not specified [RCV004470375] Chr1:44654768 [GRCh38]
Chr1:45120440 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.217C>A (p.His73Asn) single nucleotide variant not specified [RCV004470370] Chr1:44655176 [GRCh38]
Chr1:45120848 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.493C>T (p.Arg165Trp) single nucleotide variant not specified [RCV004470374] Chr1:44654900 [GRCh38]
Chr1:45120572 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.367G>A (p.Val123Met) single nucleotide variant not specified [RCV004470371] Chr1:44655026 [GRCh38]
Chr1:45120698 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.637C>T (p.Leu213Phe) single nucleotide variant not specified [RCV004686947] Chr1:44654756 [GRCh38]
Chr1:45120428 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.127T>C (p.Trp43Arg) single nucleotide variant not specified [RCV004679773] Chr1:44660230 [GRCh38]
Chr1:45125902 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.301G>C (p.Glu101Gln) single nucleotide variant not specified [RCV004679772] Chr1:44655092 [GRCh38]
Chr1:45120764 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.167C>T (p.Ala56Val) single nucleotide variant not specified [RCV004686946] Chr1:44660190 [GRCh38]
Chr1:45125862 [GRCh37]
Chr1:1p34.1		 uncertain significance
GRCh37/hg19 1p34.1-22.2(chr1:44475302-89585894)x3 copy number gain not provided [RCV004819297] Chr1:44475302..89585894 [GRCh37]
Chr1:1p34.1-22.2		 pathogenic
NM_024587.4(TMEM53):c.757G>A (p.Val253Ile) single nucleotide variant not specified [RCV004880258] Chr1:44654636 [GRCh38]
Chr1:45120308 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.406C>T (p.Arg136Cys) single nucleotide variant not specified [RCV004880260] Chr1:44654987 [GRCh38]
Chr1:45120659 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.494G>A (p.Arg165Gln) single nucleotide variant not specified [RCV004880262] Chr1:44654899 [GRCh38]
Chr1:45120571 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.466C>T (p.Arg156Trp) single nucleotide variant not specified [RCV004880259] Chr1:44654927 [GRCh38]
Chr1:45120599 [GRCh37]
Chr1:1p34.1		 uncertain significance
NM_024587.4(TMEM53):c.827G>A (p.Arg276His) single nucleotide variant not specified [RCV004880261] Chr1:44654566 [GRCh38]
Chr1:45120238 [GRCh37]
Chr1:1p34.1		 likely benign
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:3819
Count of miRNA genes:1001
Interacting mature miRNAs:1242
Transcripts:ENST00000372235, ENST00000372237, ENST00000372242, ENST00000372243, ENST00000372244, ENST00000420706, ENST00000468117, ENST00000476724, ENST00000495630
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.

Markers in Region
WI-18517  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37145,119,878 - 45,119,995UniSTSGRCh37
Build 36144,892,465 - 44,892,582RGDNCBI36
Celera143,402,767 - 43,402,884RGD
Cytogenetic Map1p34.1UniSTS
HuRef143,234,071 - 43,234,188UniSTS
GeneMap99-GB4 RH Map1130.91UniSTS
Whitehead-RH Map1152.8UniSTS
NCBI RH Map1294.0UniSTS
SHGC-74682  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37145,120,182 - 45,120,410UniSTSGRCh37
Build 36144,892,769 - 44,892,997RGDNCBI36
Celera143,403,071 - 43,403,299RGD
Cytogenetic Map1p34.1UniSTS
HuRef143,234,375 - 43,234,603UniSTS
TNG Radiation Hybrid Map124503.0UniSTS
GeneMap99-GB4 RH Map1127.56UniSTS
NCBI RH Map1294.0UniSTS
SHGC-74702  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37145,119,941 - 45,120,061UniSTSGRCh37
Build 36144,892,528 - 44,892,648RGDNCBI36
Celera143,402,830 - 43,402,950RGD
Cytogenetic Map1p34.1UniSTS
HuRef143,234,134 - 43,234,254UniSTS
TNG Radiation Hybrid Map124503.0UniSTS
GeneMap99-GB4 RH Map1142.13UniSTS
NCBI RH Map1294.0UniSTS
AL009826  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37145,134,393 - 45,134,568UniSTSGRCh37
Build 36144,906,980 - 44,907,155RGDNCBI36
Celera143,417,282 - 43,417,457RGD
Cytogenetic Map1p34.1UniSTS
HuRef143,248,586 - 43,248,761UniSTS
SHGC-74710  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37145,119,585 - 45,119,766UniSTSGRCh37
Build 36144,892,172 - 44,892,353RGDNCBI36
Celera143,402,474 - 43,402,655RGD
Cytogenetic Map1p34.1UniSTS
HuRef143,233,778 - 43,233,959UniSTS
TNG Radiation Hybrid Map124503.0UniSTS
GeneMap99-GB4 RH Map1131.85UniSTS
NCBI RH Map1294.0UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2439 2788 2252 4973 1726 2351 6 624 1950 465 2269 7304 6470 53 3734 1 852 1744 1617 174 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001300746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001300747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001300748 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_024587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011542138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA490195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK026006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK225405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK295356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK296548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK310016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL122004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL832539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC007521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC064520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM675039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM806701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR457348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HY029536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HY108001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000372235   ⟹   ENSP00000361309
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,654,465 - 44,674,443 (-)Ensembl
Ensembl Acc Id: ENST00000372237   ⟹   ENSP00000361311
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,653,247 - 44,674,481 (-)Ensembl
Ensembl Acc Id: ENST00000372242   ⟹   ENSP00000361316
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,635,238 - 44,674,459 (-)Ensembl
Ensembl Acc Id: ENST00000372243   ⟹   ENSP00000361317
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,635,238 - 44,674,462 (-)Ensembl
Ensembl Acc Id: ENST00000372244   ⟹   ENSP00000361318
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,635,238 - 44,674,477 (-)Ensembl
Ensembl Acc Id: ENST00000420706   ⟹   ENSP00000391576
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,654,896 - 44,674,402 (-)Ensembl
Ensembl Acc Id: ENST00000468117
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,653,247 - 44,674,477 (-)Ensembl
Ensembl Acc Id: ENST00000476724
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,653,247 - 44,674,442 (-)Ensembl
Ensembl Acc Id: ENST00000495630
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,636,048 - 44,674,466 (-)Ensembl
RefSeq Acc Id: NM_001300746   ⟹   NP_001287675
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38144,653,247 - 44,674,481 (-)NCBI
CHM1_1145,234,828 - 45,256,190 (-)NCBI
T2T-CHM13v2.0144,524,186 - 44,545,427 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001300747   ⟹   NP_001287676
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38144,653,247 - 44,674,481 (-)NCBI
CHM1_1145,234,828 - 45,256,190 (-)NCBI
T2T-CHM13v2.0144,524,186 - 44,545,427 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001300748   ⟹   NP_001287677
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38144,653,247 - 44,674,481 (-)NCBI
CHM1_1145,234,828 - 45,256,190 (-)NCBI
T2T-CHM13v2.0144,524,186 - 44,545,427 (-)NCBI
Sequence:
RefSeq Acc Id: NM_024587   ⟹   NP_078863
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38144,653,247 - 44,674,481 (-)NCBI
GRCh37145,118,920 - 45,140,253 (-)NCBI
Build 36144,892,088 - 44,912,686 (-)NCBI Archive
Celera143,402,390 - 43,422,988 (-)RGD
HuRef143,233,694 - 43,254,292 (-)ENTREZGENE
CHM1_1145,234,828 - 45,256,190 (-)NCBI
T2T-CHM13v2.0144,524,186 - 44,545,427 (-)NCBI
Sequence:
RefSeq Acc Id: NP_078863   ⟸   NM_024587
- Peptide Label: isoform 1
- UniProtKB: Q6IA07 (UniProtKB/Swiss-Prot),   Q5JPH2 (UniProtKB/Swiss-Prot),   B4DKG0 (UniProtKB/Swiss-Prot),   Q9H6E2 (UniProtKB/Swiss-Prot),   Q6P2H8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001287675   ⟸   NM_001300746
- Peptide Label: isoform 2
- UniProtKB: Q6P2H8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001287677   ⟸   NM_001300748
- Peptide Label: isoform 4
- UniProtKB: Q6P2H8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001287676   ⟸   NM_001300747
- Peptide Label: isoform 3
- UniProtKB: Q5TDE2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000361309   ⟸   ENST00000372235
Ensembl Acc Id: ENSP00000361311   ⟸   ENST00000372237
Ensembl Acc Id: ENSP00000361317   ⟸   ENST00000372243
Ensembl Acc Id: ENSP00000361316   ⟸   ENST00000372242
Ensembl Acc Id: ENSP00000361318   ⟸   ENST00000372244
Ensembl Acc Id: ENSP00000391576   ⟸   ENST00000420706

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P2H8-F1-model_v2 AlphaFold Q6P2H8 1-277 view protein structure

Promoters
RGD ID:6855310
Promoter ID:EPDNEW_H820
Type:initiation region
Name:TMEM53_1
Description:transmembrane protein 53
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38144,674,481 - 44,674,541EPDNEW
RGD ID:6785216
Promoter ID:HG_KWN:2439
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000357508,   ENST00000372235,   NM_001145636,   OTTHUMT00000021599,   OTTHUMT00000021600,   OTTHUMT00000021601,   OTTHUMT00000021602,   OTTHUMT00000021603,   OTTHUMT00000021604,   OTTHUMT00000021605,   OTTHUMT00000021607,   OTTHUMT00000021608,   OTTHUMT00000023115,   OTTHUMT00000023116,   OTTHUMT00000023124,   OTTHUMT00000023125,   OTTHUMT00000023126,   OTTHUMT00000023127,   OTTHUMT00000023128,   OTTHUMT00000023129,   UC009VXH.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36144,911,376 - 44,913,062 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:26186 AgrOrtholog
COSMIC TMEM53 COSMIC
Ensembl Genes ENSG00000126106 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000372235 ENTREZGENE
  ENST00000372235.7 UniProtKB/TrEMBL
  ENST00000372237 ENTREZGENE
  ENST00000372237.8 UniProtKB/Swiss-Prot
  ENST00000372242.7 UniProtKB/TrEMBL
  ENST00000372243.7 UniProtKB/TrEMBL
  ENST00000372244.3 UniProtKB/TrEMBL
  ENST00000420706.1 UniProtKB/TrEMBL
  ENST00000476724 ENTREZGENE
Gene3D-CATH 3.40.50.1820 UniProtKB/Swiss-Prot
GTEx ENSG00000126106 GTEx
HGNC ID HGNC:26186 ENTREZGENE
Human Proteome Map TMEM53 Human Proteome Map
InterPro AB_hydrolase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF829_TMEM53 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:79639 UniProtKB/Swiss-Prot
NCBI Gene 79639 ENTREZGENE
OMIM 619722 OMIM
PANTHER PTHR12265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 53 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF829 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142670769 PharmGKB
Superfamily-SCOP SSF53474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B4DKG0 ENTREZGENE
  Q5JPH2 ENTREZGENE
  Q5TDE2 ENTREZGENE, UniProtKB/TrEMBL
  Q5TDE3_HUMAN UniProtKB/TrEMBL
  Q5TDE4_HUMAN UniProtKB/TrEMBL
  Q5TDE5_HUMAN UniProtKB/TrEMBL
  Q5TDE6_HUMAN UniProtKB/TrEMBL
  Q6IA07 ENTREZGENE
  Q6P2H8 ENTREZGENE
  Q9H6E2 ENTREZGENE
  TMM53_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary B4DKG0 UniProtKB/Swiss-Prot
  Q5JPH2 UniProtKB/Swiss-Prot
  Q6IA07 UniProtKB/Swiss-Prot
  Q9H6E2 UniProtKB/Swiss-Prot