LHX1 (LIM homeobox 1) - Rat Genome Database

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Gene: LHX1 (LIM homeobox 1) Homo sapiens
Analyze
Symbol: LHX1
Name: LIM homeobox 1
RGD ID: 732963
HGNC Page HGNC
Description: Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including animal organ development; gastrulation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including animal organ development; endoderm development; and somite rostral/caudal axis specification. Predicted to be part of chromatin and protein-containing complex. Predicted to be active in nucleus.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: hLim-1; homeobox protein Lim-1; LIM homeobox protein 1; LIM-1; LIM/homeobox protein Lhx1; LIM1; MGC126723; MGC138141
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
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
GRCh38.p13 Ensembl1736,936,785 - 36,944,612 (+)EnsemblGRCh38hg38GRCh38
GRCh381736,937,475 - 36,944,612 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371735,294,772 - 35,301,912 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361732,368,612 - 32,374,607 (+)NCBINCBI36hg18NCBI36
Build 341732,368,611 - 32,374,607NCBI
Celera1732,116,628 - 32,122,623 (+)NCBI
Cytogenetic Map17q12NCBI
HuRef1731,230,715 - 31,237,858 (+)NCBIHuRef
CHM1_11735,329,038 - 35,336,178 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure formation involved in morphogenesis  (ISO,ISS)
anatomical structure morphogenesis  (ISO,ISS)
animal organ morphogenesis  (TAS)
anterior/posterior axis specification  (ISO,ISS)
anterior/posterior pattern specification  (ISO,ISS)
branching involved in ureteric bud morphogenesis  (IEA,ISO)
cell differentiation  (ISO)
cell-cell signaling  (ISO,ISS)
cellular response to fibroblast growth factor stimulus  (IEA)
cerebellar Purkinje cell differentiation  (ISO,ISS)
cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation  (ISO,ISS)
cerebellum development  (ISO,ISS)
cervix development  (ISS)
comma-shaped body morphogenesis  (ISS)
dorsal spinal cord interneuron posterior axon guidance  (ISS)
dorsal/ventral pattern formation  (ISO,ISS)
ectoderm formation  (ISO,ISS)
embryonic pattern specification  (ISO,ISS)
embryonic retina morphogenesis in camera-type eye  (ISS)
embryonic viscerocranium morphogenesis  (ISS)
endoderm development  (ISO)
endoderm formation  (ISO,ISS)
epithelium development  (ISS)
forebrain regionalization  (ISO,ISS)
gastrulation with mouth forming second  (ISO,ISS)
head development  (ISO,ISS)
horizontal cell localization  (IEA)
kidney development  (ISO,ISS)
lateral motor column neuron migration  (ISS)
mesendoderm development  (IEA,ISO)
mesonephric duct development  (IEA)
mesonephric tubule development  (ISO)
mesonephros development  (ISO)
metanephric comma-shaped body morphogenesis  (IEA)
metanephric glomerulus development  (IEA)
metanephric part of ureteric bud development  (IEA)
metanephric renal vesicle morphogenesis  (IEA,ISO)
metanephric S-shaped body morphogenesis  (IEA,ISO)
metanephros development  (ISO)
motor neuron axon guidance  (ISS)
negative regulation of transcription, DNA-templated  (ISS)
nephric duct elongation  (IEA)
nephric duct morphogenesis  (ISS)
nervous system development  (TAS)
neuron differentiation  (IBA)
oviduct development  (ISS)
oviduct epithelium development  (ISS)
paramesonephric duct development  (ISS)
pattern specification process  (ISO,ISS)
positive regulation of anterior head development  (ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (ISS)
positive regulation of embryonic development  (ISS)
positive regulation of gastrulation  (ISS)
positive regulation of nephron tubule epithelial cell differentiation  (ISS)
positive regulation of transcription, DNA-templated  (ISS)
post-embryonic development  (ISO,ISS)
primitive streak formation  (ISO,ISS)
pronephros development  (IEA,ISO)
regulation of gene expression  (ISO,ISS)
regulation of transcription by RNA polymerase II  (IBA)
renal vesicle morphogenesis  (ISS)
retina development in camera-type eye  (ISO)
retina layer formation  (ISO,ISS)
S-shaped body morphogenesis  (ISS)
somite rostral/caudal axis specification  (IEA,ISO)
spinal cord association neuron differentiation  (ISS)
spinal cord development  (ISO)
telencephalon development  (IEA,ISO)
transcription by RNA polymerase II  (ISS)
ureter morphogenesis  (IEA,ISO)
ureteric bud development  (ISO,ISS)
urogenital system development  (ISO,ISS)
uterine epithelium development  (ISS)
uterus development  (ISS)
vagina development  (ISS)
ventral spinal cord development  (IEA,ISO)

Cellular Component

References

Additional References at PubMed
PMID:8954926   PMID:9212161   PMID:9452425   PMID:9890059   PMID:10623575   PMID:11882901   PMID:12438757   PMID:12477932   PMID:12642491   PMID:15489334   PMID:16022279   PMID:16625196  
PMID:19615554   PMID:19849868   PMID:19889212   PMID:20797712   PMID:21132009   PMID:21778788   PMID:21873635   PMID:22217964   PMID:22231913   PMID:22740494   PMID:22875024   PMID:23954021  
PMID:26186194   PMID:28061432   PMID:28473536   PMID:28514442   PMID:28600106   PMID:30021884   PMID:30076415   PMID:32296183   PMID:32393512   PMID:33961781  


Genomics

Comparative Map Data
LHX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1736,936,785 - 36,944,612 (+)EnsemblGRCh38hg38GRCh38
GRCh381736,937,475 - 36,944,612 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371735,294,772 - 35,301,912 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361732,368,612 - 32,374,607 (+)NCBINCBI36hg18NCBI36
Build 341732,368,611 - 32,374,607NCBI
Celera1732,116,628 - 32,122,623 (+)NCBI
Cytogenetic Map17q12NCBI
HuRef1731,230,715 - 31,237,858 (+)NCBIHuRef
CHM1_11735,329,038 - 35,336,178 (+)NCBICHM1_1
Lhx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391184,408,801 - 84,416,360 (-)NCBIGRCm39mm39
GRCm39 Ensembl1184,409,110 - 84,416,361 (-)Ensembl
GRCm381184,517,975 - 84,525,534 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1184,518,284 - 84,525,535 (-)EnsemblGRCm38mm10GRCm38
MGSCv371184,332,881 - 84,339,036 (-)NCBIGRCm37mm9NCBIm37
MGSCv361184,335,574 - 84,341,729 (-)NCBImm8
Celera1194,132,193 - 94,138,348 (-)NCBICelera
Cytogenetic Map11CNCBI
cM Map1151.31NCBI
Lhx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21069,396,829 - 69,403,617 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1069,396,829 - 69,403,617 (-)Ensembl
Rnor_6.01071,843,991 - 71,849,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1071,843,991 - 71,849,293 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,752,917 - 71,758,219 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41072,800,497 - 72,805,799 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11072,814,866 - 72,820,169 (-)NCBI
Celera1068,324,814 - 68,330,116 (-)NCBICelera
Cytogenetic Map10q26NCBI
Lhx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554511,037,825 - 1,048,501 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554511,037,936 - 1,048,501 (-)NCBIChiLan1.0ChiLan1.0
LHX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11720,430,618 - 20,437,751 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1720,430,618 - 20,437,751 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01720,134,308 - 20,140,652 (-)NCBIMhudiblu_PPA_v0panPan3
LHX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1936,760,890 - 36,768,345 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl936,761,826 - 36,768,164 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha935,986,818 - 35,993,342 (+)NCBI
ROS_Cfam_1.0937,571,199 - 37,577,732 (+)NCBI
UMICH_Zoey_3.1936,353,003 - 36,359,535 (+)NCBI
UNSW_CanFamBas_1.0936,640,659 - 36,647,196 (+)NCBI
UU_Cfam_GSD_1.0936,727,884 - 36,734,417 (+)NCBI
Lhx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560235,742,907 - 35,750,671 (+)NCBI
SpeTri2.0NW_0049364901,324,378 - 1,332,177 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1238,450,708 - 38,456,139 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11238,450,708 - 38,457,583 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21240,067,286 - 40,073,812 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LHX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11630,843,062 - 30,850,182 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1630,842,652 - 30,849,465 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660771,575,851 - 1,584,088 (-)NCBIVero_WHO_p1.0
Lhx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248713,954,490 - 3,961,861 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH71201  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371735,300,232 - 35,300,358UniSTSGRCh37
Build 361732,374,345 - 32,374,471RGDNCBI36
Celera1732,122,361 - 32,122,487RGD
Cytogenetic Map17q12UniSTS
HuRef1731,236,175 - 31,236,301UniSTS
GeneMap99-GB4 RH Map17302.47UniSTS
NCBI RH Map17363.3UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1727
Count of miRNA genes:898
Interacting mature miRNAs:1112
Transcripts:ENST00000254457, ENST00000557970, ENST00000559335, ENST00000559572, ENST00000589584
Prediction methods:Miranda, Rnahybrid, Targetscan
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 2 6 3 3 13 7 482 64 38 27 2 1
Low 41 11 21 12 30 15 189 14 402 87 106 102 5 10 1
Below cutoff 680 1010 633 133 846 82 1209 575 2006 11 604 550 53 332 786

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000614239   ⟹   ENSP00000477829
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1736,937,475 - 36,944,612 (+)Ensembl
RefSeq Acc Id: ENST00000616237
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1736,938,460 - 36,941,394 (+)Ensembl
RefSeq Acc Id: ENST00000619297
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1736,936,785 - 36,937,846 (+)Ensembl
RefSeq Acc Id: ENST00000619939
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1736,937,635 - 36,941,531 (+)Ensembl
RefSeq Acc Id: ENST00000621767   ⟹   ENSP00000481496
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1736,942,298 - 36,943,685 (+)Ensembl
RefSeq Acc Id: ENST00000673652
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1736,937,310 - 36,940,516 (+)Ensembl
RefSeq Acc Id: NM_005568   ⟹   NP_005559
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381736,937,475 - 36,944,612 (+)NCBI
GRCh371735,294,772 - 35,301,915 (+)ENTREZGENE
Build 361732,368,612 - 32,374,607 (+)NCBI Archive
HuRef1731,230,715 - 31,237,858 (+)ENTREZGENE
CHM1_11735,329,038 - 35,336,178 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_005559   ⟸   NM_005568
- UniProtKB: P48742 (UniProtKB/Swiss-Prot),   Q58F18 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000481496   ⟸   ENST00000621767
RefSeq Acc Id: ENSP00000477829   ⟸   ENST00000614239
Protein Domains
Homeobox   LIM zinc-binding

Promoters
RGD ID:6814605
Promoter ID:HG_XEF:3354
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3
Transcripts:NM_001105447
Position:
Human AssemblyChrPosition (strand)Source
Build 361732,367,161 - 32,367,661 (+)MPROMDB
RGD ID:7234739
Promoter ID:EPDNEW_H23114
Type:initiation region
Name:LHX1_1
Description:LIM homeobox 1
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
GRCh381736,938,509 - 36,938,569EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2
pathogenic
GRCh37/hg19 17q12(chr17:34508117-36248918)x3 copy number gain See cases [RCV000050286] Chr17:34508117..36248918 [GRCh37]
Chr17:31474518..33323031 [NCBI36]
Chr17:17q12
pathogenic|conflicting data from submitters
GRCh37/hg19 17q12(chr17:34856055-36248918)x1 copy number loss See cases [RCV000050449] Chr17:34856055..36248918 [GRCh37]
Chr17:31930168..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36500215-37889296)x3 copy number gain See cases [RCV000050448] Chr17:36500215..37889296 [GRCh38]
Chr17:34856055..36248918 [GRCh37]
Chr17:31930168..33323031 [NCBI36]
Chr17:17q12
pathogenic|conflicting interpretations of pathogenicity|uncertain significance|conflicting data from submitters
GRCh37/hg19 17q12(chr17:34611352-36248918)x3 copy number gain See cases [RCV000051076] Chr17:34611352..36248918 [GRCh37]
Chr17:31635465..33323031 [NCBI36]
Chr17:17q12
pathogenic|conflicting interpretations of pathogenicity|uncertain significance|conflicting data from submitters
GRCh38/hg38 17q12(chr17:36357258-37889296)x1 copy number loss See cases [RCV000051077] Chr17:36357258..37889296 [GRCh38]
Chr17:34611352..36248918 [GRCh37]
Chr17:31635465..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3
pathogenic
GRCh38/hg38 17q12(chr17:36422657-37890225)x1 copy number loss See cases [RCV000054376] Chr17:36422657..37890225 [GRCh38]
Chr17:34768966..36263019 [GRCh37]
Chr17:31843079..33373530 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36493974-37890225)x1 copy number loss See cases [RCV000054378] Chr17:36493974..37890225 [GRCh38]
Chr17:34849818..36263019 [GRCh37]
Chr17:31923931..33346418 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36500015-37889437)x3 copy number gain See cases [RCV000054380] Chr17:36500015..37889437 [GRCh38]
Chr17:34855855..36249059 [GRCh37]
Chr17:31929968..33323172 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34855855-36249059)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054381]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054381]|See cases [RCV000054381] Chr17:34855855..36249059 [GRCh37]
Chr17:31929968..33323172 [NCBI36]
Chr17:17q12
pathogenic
NM_005568.4(LHX1):c.357A>T (p.Leu119=) single nucleotide variant Malignant melanoma [RCV000063197] Chr17:36940476 [GRCh38]
Chr17:35297773 [GRCh37]
Chr17:32371886 [NCBI36]
Chr17:17q12
not provided
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1
pathogenic
GRCh37/hg19 17q12(chr17:34450405-36248918)x1 copy number loss See cases [RCV000133661] Chr17:34450405..36248918 [GRCh37]
Chr17:31474518..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:35076189-36248926)x1 copy number loss See cases [RCV000134125] Chr17:35076189..36248926 [GRCh37]
Chr17:32150302..33323039 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34508117-36248918)x3 copy number gain See cases [RCV000148166] Chr17:34508117..36248918 [GRCh37]
Chr17:31474518..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34817422-36188700)x1 copy number loss See cases [RCV000137917] Chr17:34817422..36188700 [GRCh37]
Chr17:31891535..33262813 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36446545-38225796)x1 copy number loss See cases [RCV000137918] Chr17:36446545..38225796 [GRCh38]
Chr17:34817422..36263019 [GRCh37]
Chr17:31891535..33635633 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36357258-38225796)x3 copy number gain See cases [RCV000138816] Chr17:36357258..38225796 [GRCh38]
Chr17:34611352..36263019 [GRCh37]
Chr17:31635465..33635633 [NCBI36]
Chr17:17q12
likely pathogenic
GRCh38/hg38 17q12(chr17:36500465-37889304)x1 copy number loss See cases [RCV000138632] Chr17:36500465..37889304 [GRCh38]
Chr17:34856305..36248926 [GRCh37]
Chr17:31930418..33323039 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36461608-37889296)x3 copy number gain See cases [RCV000138608] Chr17:36461608..37889296 [GRCh38]
Chr17:34817422..36248918 [GRCh37]
Chr17:31891535..33323031 [NCBI36]
Chr17:17q12
likely pathogenic|uncertain significance
GRCh37/hg19 17q12(chr17:34817422-36248918)x1 copy number loss See cases [RCV000138609] Chr17:34817422..36248918 [GRCh37]
Chr17:31891535..33323031 [NCBI36]
Chr17:17q12
pathogenic|conflicting data from submitters
GRCh37/hg19 17q12(chr17:34360168-36248859)x1 copy number loss See cases [RCV000140228] Chr17:34360168..36248859 [GRCh37]
Chr17:31384281..33322972 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34856055-36248859)x3 copy number gain See cases [RCV000141116] Chr17:34856055..36248859 [GRCh37]
Chr17:31930168..33322972 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34856055-36248859)x1 copy number loss See cases [RCV000141117] Chr17:34856055..36248859 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822466-36393628)x1 copy number loss See cases [RCV000142004] Chr17:34822466..36393628 [GRCh37]
Chr17:31896579..33647435 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34437482-36244358)x3 copy number gain See cases [RCV000141832] Chr17:34437482..36244358 [GRCh37]
Chr17:31461595..33318471 [NCBI36]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34817452-36168075)x3 copy number gain See cases [RCV000141558] Chr17:34817452..36168075 [GRCh37]
Chr17:31891565..33242188 [NCBI36]
Chr17:17q12
uncertain significance
GRCh37/hg19 17q12(chr17:34822466-36307773)x1 copy number loss See cases [RCV000142028] Chr17:34822466..36307773 [GRCh37]
Chr17:31896579..33337163 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36350005)x3 copy number gain See cases [RCV000142072] Chr17:34822465..36350005 [GRCh37]
Chr17:31896578..33337163 [NCBI36]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34822466-36283612)x1 copy number loss See cases [RCV000142090] Chr17:34822466..36283612 [GRCh37]
Chr17:31896579..33337163 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822466-36316161)x1 copy number loss See cases [RCV000142104] Chr17:34822466..36316161 [GRCh37]
Chr17:31896579..33337163 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36283807)x1 copy number loss See cases [RCV000142180] Chr17:34822465..36283807 [GRCh37]
Chr17:31896578..33337163 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36283612)x3 copy number gain See cases [RCV000143663] Chr17:34822465..36283612 [GRCh37]
Chr17:31896578..33337163 [NCBI36]
Chr17:17q12
likely pathogenic
GRCh38/hg38 17q12(chr17:36357258-37889296)x1 copy number loss See cases [RCV000148256] Chr17:36357258..37889296 [GRCh38]
Chr17:34611352..36248918 [GRCh37]
Chr17:31635465..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36500215-37889296)x1 copy number loss See cases [RCV000148120] Chr17:36500215..37889296 [GRCh38]
Chr17:34856055..36248918 [GRCh37]
Chr17:31930168..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh38/hg38 17q12(chr17:36357258-37889296)x3 copy number gain See cases [RCV000148124] Chr17:36357258..37889296 [GRCh38]
Chr17:34611352..36248918 [GRCh37]
Chr17:31635465..33323031 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34856055-36248918)x3 copy number gain See cases [RCV000148172] Chr17:34856055..36248918 [GRCh37]
Chr17:31930168..33323031 [NCBI36]
Chr17:17q12
pathogenic
NC_000017.10:g.(34360227_34437475)_(36214026_36473024)del deletion Chromosome 17q12 deletion syndrome [RCV000191150] Chr17:34437475..36214026 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34508117-36173763)x1 copy number loss See cases [RCV000054375] Chr17:34508117..36173763 [GRCh37]
Chr17:31474518..33247876 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34849849-36151346)x1 copy number loss See cases [RCV000240223] Chr17:34849849..36151346 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34899836-36177728)x1 copy number loss See cases [RCV000051228] Chr17:34899836..36177728 [GRCh37]
Chr17:31973949..33251841 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34310998-36297053)x3 copy number gain See cases [RCV000051912] Chr17:34310998..36297053 [GRCh37]
Chr17:31335111..33373530 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34360168-36209228)x3 copy number gain See cases [RCV000051914] Chr17:34360168..36209228 [GRCh37]
Chr17:31384281..33283341 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34815184-36209228)x3 copy number gain See cases [RCV000051915] Chr17:34815184..36209228 [GRCh37]
Chr17:31889297..33283341 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34817422-36173763)x3 copy number gain See cases [RCV000051916] Chr17:34817422..36173763 [GRCh37]
Chr17:31891535..33247876 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34817422-36168104)x1 copy number loss See cases [RCV000054377] Chr17:34817422..36168104 [GRCh37]
Chr17:31891535..33242217 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34851537-36173763)x1 copy number loss See cases [RCV000054379] Chr17:34851537..36173763 [GRCh37]
Chr17:31925650..33247876 [NCBI36]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34899836-36224189)x1 copy number loss See cases [RCV000054382] Chr17:34899836..36224189 [GRCh37]
Chr17:31973949..33298302 [NCBI36]
Chr17:17q12
pathogenic
Single allele duplication Autism spectrum disorder [RCV000225391] Chr17:34815551..36249800 [GRCh37]
Chr17:17q12
pathogenic|likely pathogenic
GRCh37/hg19 17q12(chr17:34815551-36220373)x3 copy number gain Premature ovarian failure [RCV000225163] Chr17:34815551..36220373 [GRCh37]
Chr17:17q12
uncertain significance
GRCh37/hg19 17q12(chr17:34849849-36151346)x3 copy number gain See cases [RCV000240094] Chr17:34849849..36151346 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34815072-36192492)x1 deletion Chromosome 17q12 deletion syndrome [RCV000416291] Chr17:34815072..36192492 [GRCh37]
Chr17:17q12
pathogenic|uncertain significance
GRCh37/hg19 17q12(chr17:34822465-36307773)x3 copy number gain See cases [RCV000449357] Chr17:34822465..36307773 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36351919)x3 copy number gain See cases [RCV000449434] Chr17:34822465..36351919 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34815551-36208392)x1 copy number loss VATER association [RCV000522672] Chr17:34815551..36208392 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34849849-36151287)x3 copy number gain See cases [RCV000446641] Chr17:34849849..36151287 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36283612)x1 copy number loss See cases [RCV000447417] Chr17:34822465..36283612 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36283807)x1 copy number loss See cases [RCV000448533] Chr17:34822465..36283807 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34425362-36410559)x3 copy number gain See cases [RCV000447719] Chr17:34425362..36410559 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36244358)x3 copy number gain See cases [RCV000512116] Chr17:34822465..36244358 [GRCh37]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34822465-36300630)x1 copy number loss See cases [RCV000510401] Chr17:34822465..36300630 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822466-36244358)x1 copy number loss See cases [RCV000510257] Chr17:34822466..36244358 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34437482-36404555)x3 copy number gain See cases [RCV000510217] Chr17:34437482..36404555 [GRCh37]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34822465-36316161)x1 copy number loss See cases [RCV000510588] Chr17:34822465..36316161 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822467-36307773)x1 copy number loss See cases [RCV000511448] Chr17:34822467..36307773 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34437482-36350584)x3 copy number gain See cases [RCV000511415] Chr17:34437482..36350584 [GRCh37]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938) copy number gain See cases [RCV000511439] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36410559)x3 copy number gain See cases [RCV000511856] Chr17:34822465..36410559 [GRCh37]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34822466-36300466)x1 copy number loss See cases [RCV000511202] Chr17:34822466..36300466 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36397323)x1 copy number loss See cases [RCV000511069] Chr17:34822465..36397323 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36225988)x3 copy number gain See cases [RCV000511229] Chr17:34822465..36225988 [GRCh37]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34822466-36404136)x1 copy number loss See cases [RCV000511092] Chr17:34822466..36404136 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822466-36351934)x1 copy number loss See cases [RCV000510732] Chr17:34822466..36351934 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34447113-36283612)x1 copy number loss See cases [RCV000510761] Chr17:34447113..36283612 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34475679-36283612)x1 copy number loss See cases [RCV000510867] Chr17:34475679..36283612 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36244358)x1 copy number loss See cases [RCV000511282] Chr17:34822465..36244358 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36316144)x1 copy number loss See cases [RCV000510825] Chr17:34822465..36316144 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34815551-36244358)x1 copy number loss See cases [RCV000515600] Chr17:34815551..36244358 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36307773)x1 copy number loss See cases [RCV000512367] Chr17:34822465..36307773 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822466-36283807)x1 copy number loss See cases [RCV000512433] Chr17:34822466..36283807 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3 copy number gain See cases [RCV000512441] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17q12(chr17:34611352-36248918) copy number gain Elevated serum creatine phosphokinase [RCV000626519] Chr17:34611352..36248918 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34425362-36283612)x3 copy number gain not provided [RCV000683920] Chr17:34425362..36283612 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34426244-36225988)x3 copy number gain not provided [RCV000683921] Chr17:34426244..36225988 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34477385-36404555)x1 copy number loss not provided [RCV000683923] Chr17:34477385..36404555 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36244332)x3 copy number gain not provided [RCV000683924] Chr17:34822465..36244332 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36244358)x1 copy number loss not provided [RCV000683925] Chr17:34822465..36244358 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36316161)x3 copy number gain not provided [RCV000683929] Chr17:34822465..36316161 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36351919)x3 copy number gain not provided [RCV000683930] Chr17:34822465..36351919 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36371146)x3 copy number gain not provided [RCV000683931] Chr17:34822465..36371146 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36404136)x1 copy number loss not provided [RCV000683932] Chr17:34822465..36404136 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34475679-36311009)x1 copy number loss not provided [RCV000683922] Chr17:34475679..36311009 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36283612)x3 copy number gain not provided [RCV000683926] Chr17:34822465..36283612 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36283807)x1 copy number loss not provided [RCV000683927] Chr17:34822465..36283807 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36307773)x1 copy number loss not provided [RCV000683928] Chr17:34822465..36307773 [GRCh37]
Chr17:17q12
pathogenic
NC_000017.10:g.(?_34856670)_(35478412_?)del deletion Hyperphosphatasia with mental retardation syndrome 5 [RCV000707810] Chr17:34856670..35478412 [GRCh37]
Chr17:17q12
uncertain significance
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3 copy number gain not provided [RCV000739324] Chr17:8547..81060040 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3 copy number gain not provided [RCV000739320] Chr17:7214..81058310 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3 copy number gain not provided [RCV000739325] Chr17:12344..81057996 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
NC_000017.11:g.(?_36357256)_(37995300_?)del deletion Schizophrenia [RCV000754204] Chr17:36357256..37995300 [GRCh38]
Chr17:17q12
pathogenic
NC_000017.11:g.(?_36143765)_(37995300_?)del deletion Autistic disorder of childhood onset [RCV000754203] Chr17:36143765..37995300 [GRCh38]
Chr17:17q12
pathogenic
Single allele duplication Autistic disorder of childhood onset [RCV000754205] Chr17:36357256..37995300 [GRCh38]
Chr17:17q12
likely pathogenic
NC_000017.11:g.(?_36446252)_(37887875_?)del deletion Autistic disorder of childhood onset [RCV000754206] Chr17:36446252..37887875 [GRCh38]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34812294-36272082)x3 copy number gain not provided [RCV000752026] Chr17:34812294..36272082 [GRCh37]
Chr17:17q12
uncertain significance
GRCh37/hg19 17q12(chr17:34813067-36223325)x3 copy number gain not provided [RCV000752027] Chr17:34813067..36223325 [GRCh37]
Chr17:17q12
uncertain significance
GRCh37/hg19 17q12(chr17:34815551-36244358)x1 copy number loss not provided [RCV000752028] Chr17:34815551..36244358 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34815551-36307189)x1 copy number loss not provided [RCV000752029] Chr17:34815551..36307189 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34819191-36104803) copy number gain Chromosome 17q12 duplication syndrome [RCV000767659] Chr17:34819191..36104803 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34437475-36214026) copy number gain Chromosome 17q12 duplication syndrome [RCV000767740] Chr17:34437475..36214026 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34842059-36214026) copy number gain Chromosome 17q12 duplication syndrome [RCV000767688] Chr17:34842059..36214026 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34848678-36194230) copy number gain Chromosome 17q12 duplication syndrome [RCV000767620] Chr17:34848678..36194230 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34819191-36194230) copy number loss Chromosome 17q12 deletion syndrome [RCV000767697] Chr17:34819191..36194230 [GRCh37]
Chr17:17q12
pathogenic
Single allele deletion Neurodevelopmental disorder [RCV000787391] Chr17:34815172..36249799 [GRCh37]
Chr17:17q12
uncertain significance
GRCh37/hg19 17p11.2-q21.2(chr17:21690653-38772647)x3 copy number gain not provided [RCV000846852] Chr17:21690653..38772647 [GRCh37]
Chr17:17p11.2-q21.2
pathogenic
GRCh37/hg19 17q12(chr17:35258617-35825367)x3 copy number gain not provided [RCV001006896] Chr17:35258617..35825367 [GRCh37]
Chr17:17q12
uncertain significance
GRCh37/hg19 17q12(chr17:34815551-36244358)x3 copy number gain See cases [RCV001194546] Chr17:34815551..36244358 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34822465-36410559)x3 copy number gain not provided [RCV001259334] Chr17:34822465..36410559 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34815466-36249366)x3 copy number gain not provided [RCV001537910] Chr17:34815466..36249366 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34841190-35733119) copy number gain Autism with high cognitive abilities [RCV001291968] Chr17:34841190..35733119 [GRCh37]
Chr17:17q12
likely pathogenic
GRCh37/hg19 17q12(chr17:34817422-36243028) copy number gain Positional foot deformity [RCV001291945] Chr17:34817422..36243028 [GRCh37]
Chr17:17q12
pathogenic
GRCh37/hg19 17q12(chr17:34437475-36243028) copy number gain Polyhydramnios [RCV001291974] Chr17:34437475..36243028 [GRCh37]
Chr17:17q12
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:6593 AgrOrtholog
COSMIC LHX1 COSMIC
Ensembl Genes ENSG00000273706 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000274577 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000477829 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000481496 UniProtKB/TrEMBL
  ENSP00000484449 UniProtKB/Swiss-Prot
  ENSP00000488248 UniProtKB/TrEMBL
Ensembl Transcript ENST00000614239 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000620305 UniProtKB/Swiss-Prot
  ENST00000621767 UniProtKB/TrEMBL
  ENST00000633397 UniProtKB/TrEMBL
GTEx ENSG00000273706 GTEx
  ENSG00000274577 GTEx
HGNC ID HGNC:6593 ENTREZGENE
Human Proteome Map LHX1 Human Proteome Map
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:3975 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 3975 ENTREZGENE
OMIM 601999 OMIM
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA30364 PharmGKB
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WY40_HUMAN UniProtKB/TrEMBL
  A0A0J9YX49_HUMAN UniProtKB/TrEMBL
  LHX1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q58F18 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q3MIW0 UniProtKB/Swiss-Prot