LGI2 (leucine rich repeat LGI family member 2) - Rat Genome Database

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Gene: LGI2 (leucine rich repeat LGI family member 2) Homo sapiens
Analyze
Symbol: LGI2
Name: leucine rich repeat LGI family member 2
RGD ID: 1321270
HGNC Page HGNC:18710
Description: Predicted to be involved in inhibitory synapse assembly. Predicted to be located in extracellular region.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: FLJ10675; KIAA1916; leucine-rich glioma-inactivated protein 2; leucine-rich repeat LGI family member 2; leucine-rich repeat LGI family, member 2; leucine-rich, glioma inactivated 2; LGI1-like protein 2; LGIL2; MGC126808; MGC126810
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
GRCh38424,992,081 - 25,030,946 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl424,998,847 - 25,030,946 (-)EnsemblGRCh38hg38GRCh38
GRCh37425,000,469 - 25,032,568 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36424,612,488 - 24,641,413 (-)NCBINCBI36Build 36hg18NCBI36
Build 34424,679,658 - 24,708,584NCBI
Celera425,449,352 - 25,481,288 (-)NCBICelera
Cytogenetic Map4p15.2NCBI
HuRef424,341,380 - 24,373,316 (-)NCBIHuRef
CHM1_1424,999,825 - 25,031,778 (-)NCBICHM1_1
T2T-CHM13v2.0424,973,998 - 25,012,867 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
epilepsy  (ISO)
genetic disease  (IAGP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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:8619474   PMID:9110174   PMID:11572484   PMID:12023020   PMID:12095917   PMID:12217514   PMID:12477932   PMID:14702039   PMID:15489334   PMID:16014869   PMID:16021519   PMID:20183877  
PMID:20863412   PMID:21873635   PMID:33961781  


Genomics

Comparative Map Data
LGI2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38424,992,081 - 25,030,946 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl424,998,847 - 25,030,946 (-)EnsemblGRCh38hg38GRCh38
GRCh37425,000,469 - 25,032,568 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36424,612,488 - 24,641,413 (-)NCBINCBI36Build 36hg18NCBI36
Build 34424,679,658 - 24,708,584NCBI
Celera425,449,352 - 25,481,288 (-)NCBICelera
Cytogenetic Map4p15.2NCBI
HuRef424,341,380 - 24,373,316 (-)NCBIHuRef
CHM1_1424,999,825 - 25,031,778 (-)NCBICHM1_1
T2T-CHM13v2.0424,973,998 - 25,012,867 (-)NCBIT2T-CHM13v2.0
Lgi2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39552,690,859 - 52,723,689 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl552,690,859 - 52,723,804 (-)EnsemblGRCm39 Ensembl
GRCm38552,533,517 - 52,566,306 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl552,533,517 - 52,566,462 (-)EnsemblGRCm38mm10GRCm38
MGSCv37552,929,103 - 52,957,519 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36552,826,112 - 52,854,528 (-)NCBIMGSCv36mm8
Celera549,911,427 - 49,940,116 (-)NCBICelera
Cytogenetic Map5C1NCBI
cM Map528.25NCBI
Lgi2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81462,628,746 - 62,656,231 (+)NCBIGRCr8
mRatBN7.21458,415,965 - 58,443,450 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1458,415,965 - 58,443,407 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1462,821,564 - 62,849,027 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01464,135,138 - 64,162,652 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01460,531,888 - 60,559,402 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01460,764,325 - 60,791,809 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1460,764,409 - 60,796,116 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01460,876,468 - 60,903,952 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41463,184,650 - 63,212,134 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11463,158,817 - 63,214,421 (+)NCBI
Celera1457,514,048 - 57,541,516 (+)NCBICelera
Cytogenetic Map14q11NCBI
Lgi2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495548058,661 - 89,920 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495548058,661 - 89,906 (+)NCBIChiLan1.0ChiLan1.0
LGI2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2325,249,838 - 25,279,005 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1425,443,540 - 25,472,696 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0419,397,279 - 19,429,349 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1424,684,991 - 24,713,880 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl424,684,991 - 24,714,035 (-)Ensemblpanpan1.1panPan2
LGI2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1385,114,356 - 85,215,063 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl385,182,657 - 85,211,357 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha387,694,029 - 87,726,513 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0386,155,381 - 86,187,875 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl386,155,137 - 86,183,648 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1385,288,432 - 85,320,930 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0385,393,580 - 85,426,122 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0385,779,270 - 85,811,791 (+)NCBIUU_Cfam_GSD_1.0
Lgi2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528550,716,260 - 50,776,470 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364774,450,786 - 4,480,108 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364774,417,926 - 4,478,136 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LGI2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl818,986,046 - 19,017,431 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1818,986,549 - 19,017,238 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LGI2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12725,334,139 - 25,363,889 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2725,334,457 - 25,366,819 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604771,852,317 - 71,883,674 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lgi2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247557,317,445 - 7,348,236 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247557,317,471 - 7,344,003 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LGI2
26 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4p16.3-15.1(chr4:72555-28066309)x1 copy number loss See cases [RCV000051642] Chr4:72555..28066309 [GRCh38]
Chr4:72447..28067931 [GRCh37]
Chr4:62447..27677029 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-15.2(chr4:51519-26519788)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051752]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051752]|See cases [RCV000051752] Chr4:51519..26519788 [GRCh38]
Chr4:51413..26521410 [GRCh37]
Chr4:41413..26130508 [NCBI36]
Chr4:4p16.3-15.2		 pathogenic
GRCh38/hg38 4p16.3-15.1(chr4:72555-33130620)x3 copy number gain See cases [RCV000051753] Chr4:72555..33130620 [GRCh38]
Chr4:72447..33132242 [GRCh37]
Chr4:62447..32808637 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:85149-38700366)x3 copy number gain See cases [RCV000051757] Chr4:85149..38700366 [GRCh38]
Chr4:85040..38701987 [GRCh37]
Chr4:75040..38378382 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p15.31-15.2(chr4:21056309-26732162)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053263]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053263]|See cases [RCV000053263] Chr4:21056309..26732162 [GRCh38]
Chr4:21057932..26733784 [GRCh37]
Chr4:20667030..26342882 [NCBI36]
Chr4:4p15.31-15.2		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:72555-39477144)x3 copy number gain See cases [RCV000133677] Chr4:72555..39477144 [GRCh38]
Chr4:72447..39478764 [GRCh37]
Chr4:62447..39155159 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p15.2(chr4:23862000-27685546)x1 copy number loss See cases [RCV000135404] Chr4:23862000..27685546 [GRCh38]
Chr4:23863623..27687168 [GRCh37]
Chr4:23472721..27296266 [NCBI36]
Chr4:4p15.2		 pathogenic
GRCh38/hg38 4p15.32-15.1(chr4:16925022-32113076)x1 copy number loss See cases [RCV000135806] Chr4:16925022..32113076 [GRCh38]
Chr4:16926645..32114698 [GRCh37]
Chr4:16535743..31758596 [NCBI36]
Chr4:4p15.32-15.1		 pathogenic|likely pathogenic
GRCh38/hg38 4p16.3-12(chr4:36424-47491595)x3 copy number gain See cases [RCV000137261] Chr4:36424..47491595 [GRCh38]
Chr4:36424..47493612 [GRCh37]
Chr4:26424..47188369 [NCBI36]
Chr4:4p16.3-12		 pathogenic
GRCh37/hg19 4p16.3-15.1(chr4:71552-29006745)x1 copy number loss See cases [RCV000240003] Chr4:71552..29006745 [GRCh37]
Chr4:4p16.3-15.1		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:12440-49064044)x3 copy number gain See cases [RCV000240562] Chr4:12440..49064044 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p15.2-15.1(chr4:23458442-29252060)x1 copy number loss See cases [RCV000240221] Chr4:23458442..29252060 [GRCh37]
Chr4:4p15.2-15.1		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:68345-49089361)x3 copy number gain not specified [RCV003986479] Chr4:68345..49089361 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p16.3-12(chr4:114784-47569569)x3 copy number gain FETAL DEMISE [RCV002282978] Chr4:114784..47569569 [GRCh37]
Chr4:4p16.3-12		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:68345-49089361)x3 copy number gain See cases [RCV002292704] Chr4:68345..49089361 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:68345-49093788)x3 copy number gain See cases [RCV000446451] Chr4:68345..49093788 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:12440-190904441)x3 copy number gain See cases [RCV000446653] Chr4:12440..190904441 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p15.2-15.1(chr4:23790131-32302608)x1 copy number loss See cases [RCV000445756] Chr4:23790131..32302608 [GRCh37]
Chr4:4p15.2-15.1		 likely pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473) copy number gain See cases [RCV000510453] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p16.3-q13.1(chr4:68345-66440622)x3 copy number gain See cases [RCV000511193] Chr4:68345..66440622 [GRCh37]
Chr4:4p16.3-q13.1		 pathogenic
NM_018176.4(LGI2):c.29C>T (p.Ala10Val) single nucleotide variant Inborn genetic diseases [RCV003253838] Chr4:25030665 [GRCh38]
Chr4:25032287 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.77G>C (p.Arg26Pro) single nucleotide variant Inborn genetic diseases [RCV003253839] Chr4:25030617 [GRCh38]
Chr4:25032239 [GRCh37]
Chr4:4p15.2		 likely benign
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473)x3 copy number gain See cases [RCV000512241] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:68345-49089361)x3 copy number gain not provided [RCV000682363] Chr4:68345..49089361 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p16.3-15.1(chr4:4165334-33324781)x1 copy number loss not provided [RCV000682373] Chr4:4165334..33324781 [GRCh37]
Chr4:4p16.3-15.1		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190915650)x3 copy number gain not provided [RCV000743155] Chr4:49450..190915650 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190963766)x3 copy number gain not provided [RCV000743156] Chr4:49450..190963766 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:11525-191028879)x3 copy number gain not provided [RCV000743147] Chr4:11525..191028879 [GRCh37]
Chr4:4p16.3-q35.2		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:1356924-49659859)x3 copy number gain not provided [RCV000743201] Chr4:1356924..49659859 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p16.3-12(chr4:49450-46339070)x3 copy number gain not provided [RCV000743154] Chr4:49450..46339070 [GRCh37]
Chr4:4p16.3-12		 pathogenic
GRCh37/hg19 4p15.33-15.1(chr4:12778849-27760141) copy number loss not provided [RCV000767707] Chr4:12778849..27760141 [GRCh37]
Chr4:4p15.33-15.1		 pathogenic
NM_018176.4(LGI2):c.215C>T (p.Thr72Met) single nucleotide variant Inborn genetic diseases [RCV003244477] Chr4:25028561 [GRCh38]
Chr4:25030183 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.622G>A (p.Val208Met) single nucleotide variant Inborn genetic diseases [RCV003239394] Chr4:25018022 [GRCh38]
Chr4:25019644 [GRCh37]
Chr4:4p15.2		 uncertain significance
GRCh37/hg19 4p16.3-15.2(chr4:68345-27423424)x3 copy number gain not provided [RCV001005510] Chr4:68345..27423424 [GRCh37]
Chr4:4p16.3-15.2		 pathogenic
GRCh37/hg19 4p16.3-11(chr4:49450-49620898)x3 copy number gain See cases [RCV001194594] Chr4:49450..49620898 [GRCh37]
Chr4:4p16.3-11		 pathogenic
GRCh37/hg19 4p15.31-15.1(chr4:20406475-29134345)x1 copy number loss not provided [RCV001005527] Chr4:20406475..29134345 [GRCh37]
Chr4:4p15.31-15.1		 pathogenic
GRCh37/hg19 4p16.3-15.1(chr4:69671-29702595)x3 copy number gain not provided [RCV001537928] Chr4:69671..29702595 [GRCh37]
Chr4:4p16.3-15.1		 pathogenic
GRCh37/hg19 4p16.3-15.1(chr4:68345-34512694) copy number gain 4p16.3 microduplication syndrome [RCV003319592] Chr4:68345..34512694 [GRCh37]
Chr4:4p16.3-15.1		 pathogenic
GRCh37/hg19 4p15.31-14(chr4:19892850-37325128) copy number loss not specified [RCV002053409] Chr4:19892850..37325128 [GRCh37]
Chr4:4p15.31-14		 pathogenic
GRCh37/hg19 4p15.2-15.1(chr4:23790131-32302608) copy number loss not specified [RCV002053411] Chr4:23790131..32302608 [GRCh37]
Chr4:4p15.2-15.1		 likely pathogenic
NM_018176.4(LGI2):c.1132T>A (p.Phe378Ile) single nucleotide variant Inborn genetic diseases [RCV003257492] Chr4:25003957 [GRCh38]
Chr4:25005579 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.1280G>A (p.Arg427Gln) single nucleotide variant Inborn genetic diseases [RCV002970138] Chr4:25003809 [GRCh38]
Chr4:25005431 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.634G>C (p.Asp212His) single nucleotide variant Inborn genetic diseases [RCV002753302] Chr4:25018010 [GRCh38]
Chr4:25019632 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.388C>T (p.Arg130Cys) single nucleotide variant Inborn genetic diseases [RCV002771713] Chr4:25024845 [GRCh38]
Chr4:25026467 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.604G>A (p.Glu202Lys) single nucleotide variant Inborn genetic diseases [RCV002732609] Chr4:25018040 [GRCh38]
Chr4:25019662 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.1384C>T (p.Arg462Trp) single nucleotide variant Inborn genetic diseases [RCV002844436] Chr4:25003705 [GRCh38]
Chr4:25005327 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.1207A>G (p.Lys403Glu) single nucleotide variant Inborn genetic diseases [RCV002869999] Chr4:25003882 [GRCh38]
Chr4:25005504 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.779A>T (p.Asp260Val) single nucleotide variant Inborn genetic diseases [RCV002873460] Chr4:25012376 [GRCh38]
Chr4:25013998 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.389G>A (p.Arg130His) single nucleotide variant Inborn genetic diseases [RCV002698687] Chr4:25024844 [GRCh38]
Chr4:25026466 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.244T>C (p.Ser82Pro) single nucleotide variant Inborn genetic diseases [RCV002940806] Chr4:25028532 [GRCh38]
Chr4:25030154 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.1555G>A (p.Asp519Asn) single nucleotide variant Inborn genetic diseases [RCV002987879] Chr4:25003534 [GRCh38]
Chr4:25005156 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.924T>G (p.Ser308Arg) single nucleotide variant Inborn genetic diseases [RCV002836062] Chr4:25004165 [GRCh38]
Chr4:25005787 [GRCh37]
Chr4:4p15.2		 uncertain significance
GRCh38/hg38 4p15.33-14(chr4:11399082-38137335) copy number loss 4p partial monosomy syndrome [RCV003155905] Chr4:11399082..38137335 [GRCh38]
Chr4:4p15.33-14		 pathogenic
NM_018176.4(LGI2):c.916G>A (p.Asp306Asn) single nucleotide variant Inborn genetic diseases [RCV003210901] Chr4:25004173 [GRCh38]
Chr4:25005795 [GRCh37]
Chr4:4p15.2		 uncertain significance
GRCh38/hg38 4p16.3-q12(chr4:85624-57073230)x3 copy number gain Neurodevelopmental disorder [RCV003327613] Chr4:85624..57073230 [GRCh38]
Chr4:4p16.3-q12		 pathogenic
GRCh38/hg38 4p16.3-13(chr4:2904667-42963232)x3 copy number gain Neurodevelopmental disorder [RCV003327612] Chr4:2904667..42963232 [GRCh38]
Chr4:4p16.3-13		 pathogenic
GRCh38/hg38 4p16.3-11(chr4:1-49062177)x3 copy number gain Neurodevelopmental disorder [RCV003327611] Chr4:1..49062177 [GRCh38]
Chr4:4p16.3-11		 pathogenic
NM_018176.4(LGI2):c.92G>C (p.Arg31Thr) single nucleotide variant Inborn genetic diseases [RCV003379760] Chr4:25030602 [GRCh38]
Chr4:25032224 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.1258G>A (p.Val420Ile) single nucleotide variant Inborn genetic diseases [RCV003365792] Chr4:25003831 [GRCh38]
Chr4:25005453 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.692T>G (p.Val231Gly) single nucleotide variant Inborn genetic diseases [RCV003354851] Chr4:25012463 [GRCh38]
Chr4:25014085 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.810C>A (p.Asp270Glu) single nucleotide variant Inborn genetic diseases [RCV003369698] Chr4:25012345 [GRCh38]
Chr4:25013967 [GRCh37]
Chr4:4p15.2		 uncertain significance
NM_018176.4(LGI2):c.729C>T (p.Tyr243=) single nucleotide variant not provided [RCV003434990] Chr4:25012426 [GRCh38]
Chr4:25014048 [GRCh37]
Chr4:4p15.2		 likely benign
NM_018176.4(LGI2):c.348T>C (p.Ile116=) single nucleotide variant not provided [RCV003434991] Chr4:25024885 [GRCh38]
Chr4:25026507 [GRCh37]
Chr4:4p15.2		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1971
Count of miRNA genes:1043
Interacting mature miRNAs:1260
Transcripts:ENST00000382114, ENST00000512108
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
D4S2948  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37425,009,138 - 25,009,287UniSTSGRCh37
Build 36424,618,236 - 24,618,385RGDNCBI36
Celera425,458,018 - 25,458,157RGD
Cytogenetic Map4p15.2UniSTS
HuRef424,350,045 - 24,350,186UniSTS
Marshfield Genetic Map438.77RGD
Marshfield Genetic Map438.77UniSTS
Genethon Genetic Map438.2UniSTS
deCODE Assembly Map441.58UniSTS
GeneMap99-GB4 RH Map497.57UniSTS
Whitehead-YAC Contig Map4 UniSTS
RH18349  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37425,003,902 - 25,004,159UniSTSGRCh37
Build 36424,613,000 - 24,613,257RGDNCBI36
Celera425,452,783 - 25,453,040RGD
Cytogenetic Map4p15.2UniSTS
HuRef424,344,810 - 24,345,067UniSTS
GeneMap99-GB4 RH Map499.69UniSTS
D4S2724  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37425,002,425 - 25,002,577UniSTSGRCh37
Build 36424,611,523 - 24,611,675RGDNCBI36
Celera425,451,306 - 25,451,458RGD
Cytogenetic Map4p15.2UniSTS
HuRef424,343,334 - 24,343,486UniSTS
TNG Radiation Hybrid Map415305.0UniSTS
SHGC-59783  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37425,003,485 - 25,003,606UniSTSGRCh37
Build 36424,612,583 - 24,612,704RGDNCBI36
Celera425,452,366 - 25,452,487RGD
Cytogenetic Map4p15.2UniSTS
HuRef424,344,393 - 24,344,514UniSTS
GeneMap99-GB4 RH Map495.96UniSTS
LGI2__6390  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37425,003,392 - 25,004,170UniSTSGRCh37
Build 36424,612,490 - 24,613,268RGDNCBI36
Celera425,452,273 - 25,453,051RGD
HuRef424,344,301 - 24,345,078UniSTS


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 adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 568 359 13 2 53 3 676 465 754 40 150 53 24 668 1
Low 1477 1788 1091 189 350 106 2017 877 2575 257 1083 1423 87 1 1153 995 3 2
Below cutoff 320 763 598 418 878 340 1632 839 380 108 194 90 81 27 1123

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_018176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011513850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017008356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054350373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054350374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB067503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC113614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF052098 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF467955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ487516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ487958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK001537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK058023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK126093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL833647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC101759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC101761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS083233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HF548050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000382114   ⟹   ENSP00000371548
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl424,998,847 - 25,030,946 (-)Ensembl
RefSeq Acc Id: ENST00000512108   ⟹   ENSP00000426254
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl424,999,767 - 25,030,665 (-)Ensembl
RefSeq Acc Id: NM_018176   ⟹   NP_060646
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38424,998,847 - 25,030,946 (-)NCBI
GRCh37425,000,471 - 25,032,414 (-)RGD
Build 36424,612,488 - 24,641,413 (-)NCBI Archive
Celera425,449,352 - 25,481,288 (-)RGD
HuRef424,341,380 - 24,373,316 (-)RGD
CHM1_1424,999,825 - 25,031,778 (-)NCBI
T2T-CHM13v2.0424,980,764 - 25,012,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011513850   ⟹   XP_011512152
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38425,006,785 - 25,030,946 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017008356   ⟹   XP_016863845
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38424,992,081 - 25,030,946 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054350373   ⟹   XP_054206348
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0424,987,774 - 25,012,867 (-)NCBI
RefSeq Acc Id: XM_054350374   ⟹   XP_054206349
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0424,973,998 - 25,012,867 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_060646   ⟸   NM_018176
- Peptide Label: precursor
- UniProtKB: Q96PX2 (UniProtKB/Swiss-Prot),   Q8NDW6 (UniProtKB/Swiss-Prot),   Q3MIN2 (UniProtKB/Swiss-Prot),   Q9NVK4 (UniProtKB/Swiss-Prot),   Q8N0V4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011512152   ⟸   XM_011513850
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016863845   ⟸   XM_017008356
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSP00000426254   ⟸   ENST00000512108
RefSeq Acc Id: ENSP00000371548   ⟸   ENST00000382114
RefSeq Acc Id: XP_054206349   ⟸   XM_054350374
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054206348   ⟸   XM_054350373
- Peptide Label: isoform X1
Protein Domains
LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N0V4-F1-model_v2 AlphaFold Q8N0V4 1-545 view protein structure

Promoters
RGD ID:6867146
Promoter ID:EPDNEW_H6738
Type:initiation region
Name:LGI2_1
Description:leucine rich repeat LGI family member 2
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
GRCh38425,030,946 - 25,031,006EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:18710 AgrOrtholog
COSMIC LGI2 COSMIC
Ensembl Genes ENSG00000153012 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000382114 ENTREZGENE
  ENST00000382114.9 UniProtKB/Swiss-Prot
  ENST00000512108.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000153012 GTEx
HGNC ID HGNC:18710 ENTREZGENE
Human Proteome Map LGI2 Human Proteome Map
InterPro Cys-rich_flank_reg_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EAR UniProtKB/Swiss-Prot
  EPTP UniProtKB/Swiss-Prot
  Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:55203 UniProtKB/Swiss-Prot
NCBI Gene 55203 ENTREZGENE
OMIM 608301 OMIM
PANTHER LEUCINE-RICH REPEAT LGI FAMILY MEMBER 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LEUCINE-RICH REPEAT-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EPTP UniProtKB/Swiss-Prot
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA38654 PharmGKB
PROSITE EAR UniProtKB/Swiss-Prot
SMART LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Putative isomerase YbhE UniProtKB/Swiss-Prot
UniProt H0YA65_HUMAN UniProtKB/TrEMBL
  L0R890_HUMAN UniProtKB/TrEMBL
  LGI2_HUMAN UniProtKB/Swiss-Prot
  Q3MIN2 ENTREZGENE
  Q8N0V4 ENTREZGENE
  Q8NDW6 ENTREZGENE
  Q96PX2 ENTREZGENE
  Q9NVK4 ENTREZGENE
UniProt Secondary Q3MIN2 UniProtKB/Swiss-Prot
  Q8NDW6 UniProtKB/Swiss-Prot
  Q96PX2 UniProtKB/Swiss-Prot
  Q9NVK4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-14 LGI2  leucine rich repeat LGI family member 2    leucine-rich repeat LGI family member 2  Symbol and/or name change 5135510 APPROVED
2015-11-24 LGI2  leucine-rich repeat LGI family member 2    leucine-rich repeat LGI family, member 2  Symbol and/or name change 5135510 APPROVED