LIN7A (lin-7 homolog A, crumbs cell polarity complex component) - Rat Genome Database

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Gene: LIN7A (lin-7 homolog A, crumbs cell polarity complex component) Homo sapiens
Analyze
Symbol: LIN7A
Name: lin-7 homolog A, crumbs cell polarity complex component
RGD ID: 731642
HGNC Page HGNC:17787
Description: Enables L27 domain binding activity. Predicted to be involved in maintenance of epithelial cell apical/basal polarity; neurotransmitter secretion; and protein localization to basolateral plasma membrane. Predicted to act upstream of or within inner ear development and synaptic vesicle transport. Located in extracellular exosome.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: hLin-7; lin-7 homolog A; lin-7-ba; LIN-7A; LIN7; MALS-1; MALS1; mammalian LIN-7 1; mammalian lin-seven protein 1; MGC148143; tax interaction protein 33; TIP-33; veli-1; VELI1; vertebrate lin-7 homolog 1; vertebrate LIN7 homolog 1
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
GRCh381280,792,520 - 80,937,934 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1280,792,520 - 80,937,934 (-)EnsemblGRCh38hg38GRCh38
GRCh371281,186,299 - 81,331,713 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361279,715,302 - 79,855,825 (-)NCBINCBI36Build 36hg18NCBI36
Build 341279,693,638 - 79,834,162NCBI
Celera1280,857,386 - 80,997,854 (-)NCBICelera
Cytogenetic Map12q21.31NCBI
HuRef1278,248,054 - 78,388,586 (-)NCBIHuRef
CHM1_11281,157,566 - 81,298,106 (-)NCBICHM1_1
T2T-CHM13v2.01280,771,214 - 80,916,777 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (ISO)
(-)-demecolcine  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
amiodarone  (EXP)
ammonium chloride  (ISO)
aristolochic acid A  (EXP)
Benoxacor  (ISO)
benzo[a]pyrene  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Butylparaben  (ISO)
calcitriol  (EXP)
chlorpyrifos  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
coumestrol  (EXP)
crocidolite asbestos  (EXP)
cyclosporin A  (EXP)
dorsomorphin  (EXP)
doxorubicin  (EXP)
endosulfan  (ISO)
enzacamene  (ISO)
ethanol  (ISO)
fisetin  (ISO)
flavonoids  (ISO)
formaldehyde  (EXP)
FR900359  (EXP)
furan  (ISO)
geldanamycin  (EXP)
genistein  (ISO)
glafenine  (ISO)
isoprenaline  (ISO)
leflunomide  (EXP)
maneb  (ISO)
methotrexate  (EXP)
methyl methanesulfonate  (EXP)
methylmercury chloride  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (ISO)
orphenadrine  (ISO)
oxycodone  (ISO)
ozone  (ISO)
p-toluidine  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (EXP)
PhIP  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
Ptaquiloside  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (EXP)
silicon dioxide  (EXP,ISO)
sunitinib  (EXP)
Tesaglitazar  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
trichloroethene  (ISO)
trichostatin A  (EXP)
triclosan  (EXP)
urethane  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vorinostat  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9482110   PMID:9753324   PMID:10228153   PMID:10341223   PMID:10753959   PMID:11311936   PMID:12110687   PMID:12477932   PMID:14596909   PMID:14702039   PMID:14722086   PMID:14960569  
PMID:15024025   PMID:15494546   PMID:16192278   PMID:16688213   PMID:16855024   PMID:17237226   PMID:18286632   PMID:19615732   PMID:20379614   PMID:20458337   PMID:21832049   PMID:21873635  
PMID:23259602   PMID:23718855   PMID:23782696   PMID:24366813   PMID:24658322   PMID:25352737   PMID:25416956   PMID:26053890   PMID:26186194   PMID:26887652   PMID:27320196   PMID:28514442  
PMID:28675297   PMID:29229926   PMID:29749382   PMID:29997244   PMID:31515488   PMID:31871319   PMID:32296183   PMID:32707033   PMID:33001583   PMID:33961781   PMID:35271311  


Genomics

Comparative Map Data
LIN7A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381280,792,520 - 80,937,934 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1280,792,520 - 80,937,934 (-)EnsemblGRCh38hg38GRCh38
GRCh371281,186,299 - 81,331,713 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361279,715,302 - 79,855,825 (-)NCBINCBI36Build 36hg18NCBI36
Build 341279,693,638 - 79,834,162NCBI
Celera1280,857,386 - 80,997,854 (-)NCBICelera
Cytogenetic Map12q21.31NCBI
HuRef1278,248,054 - 78,388,586 (-)NCBIHuRef
CHM1_11281,157,566 - 81,298,106 (-)NCBICHM1_1
T2T-CHM13v2.01280,771,214 - 80,916,777 (-)NCBIT2T-CHM13v2.0
Lin7a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910107,107,410 - 107,261,007 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10107,107,547 - 107,257,335 (+)EnsemblGRCm39 Ensembl
GRCm3810107,271,549 - 107,425,146 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10107,271,686 - 107,421,474 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710106,708,887 - 106,862,199 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610106,675,941 - 106,829,253 (+)NCBIMGSCv36mm8
Celera10109,214,597 - 109,367,553 (+)NCBICelera
Cytogenetic Map10D1NCBI
cM Map1055.83NCBI
Lin7a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8744,473,568 - 44,629,074 (+)NCBIGRCr8
mRatBN7.2742,586,704 - 42,742,609 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl742,586,719 - 42,730,550 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0749,429,613 - 49,627,835 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl749,385,705 - 49,656,856 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0749,860,444 - 49,889,321 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4745,970,622 - 46,116,986 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1745,990,892 - 46,137,257 (+)NCBI
Celera739,460,246 - 39,603,293 (+)NCBICelera
Cytogenetic Map7q21NCBI
Lin7a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540519,413,817 - 19,548,716 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540519,403,002 - 19,548,716 (-)NCBIChiLan1.0ChiLan1.0
LIN7A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21088,840,533 - 88,988,187 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11288,836,928 - 88,984,590 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01278,312,501 - 78,456,871 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11281,423,133 - 81,567,522 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1281,442,152 - 81,567,522 (-)Ensemblpanpan1.1panPan2
LIN7A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11523,101,524 - 23,186,343 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1523,111,944 - 23,187,354 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1523,528,909 - 23,652,711 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01523,466,000 - 23,590,006 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1523,474,291 - 23,588,890 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11523,043,326 - 23,167,286 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01523,102,924 - 23,227,023 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01523,343,341 - 23,467,440 (-)NCBIUU_Cfam_GSD_1.0
Lin7a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494537,101,803 - 37,239,332 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366981,686,929 - 1,810,380 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366981,675,329 - 1,810,845 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIN7A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl5100,538,065 - 100,674,551 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.15100,533,630 - 100,686,709 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25105,473,697 - 105,629,759 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIN7A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11176,269,360 - 76,412,638 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1176,282,218 - 76,413,171 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037169,017,193 - 169,173,186 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lin7a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624837104,948 - 258,085 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LIN7A
13 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q15-21.31(chr12:70337484-81761145)x1 copy number loss See cases [RCV000051313] Chr12:70337484..81761145 [GRCh38]
Chr12:70731264..82154924 [GRCh37]
Chr12:69017531..80679055 [NCBI36]
Chr12:12q15-21.31		 pathogenic
GRCh38/hg38 12q21.31(chr12:80266605-85253555)x1 copy number loss See cases [RCV000051315] Chr12:80266605..85253555 [GRCh38]
Chr12:80660385..85647333 [GRCh37]
Chr12:79184516..84171464 [NCBI36]
Chr12:12q21.31		 pathogenic
GRCh38/hg38 12q21.31(chr12:80393097-81021534)x1 copy number loss See cases [RCV000051316] Chr12:80393097..81021534 [GRCh38]
Chr12:80786877..81415313 [GRCh37]
Chr12:79311008..79939444 [NCBI36]
Chr12:12q21.31		 pathogenic
GRCh38/hg38 12q21.31(chr12:80538484-80798086)x1 copy number loss See cases [RCV000051318] Chr12:80538484..80798086 [GRCh38]
Chr12:80932263..81191865 [GRCh37]
Chr12:79456394..79715996 [NCBI36]
Chr12:12q21.31		 pathogenic
GRCh38/hg38 12q21.2-21.31(chr12:77564757-85370822)x3 copy number gain See cases [RCV000053684] Chr12:77564757..85370822 [GRCh38]
Chr12:77958537..85764600 [GRCh37]
Chr12:76482668..84288731 [NCBI36]
Chr12:12q21.2-21.31		 pathogenic
NM_004664.2(LIN7A):c.494G>A (p.Gly165Glu) single nucleotide variant Malignant melanoma [RCV000070234] Chr12:80811673 [GRCh38]
Chr12:81205452 [GRCh37]
Chr12:79729583 [NCBI36]
Chr12:12q21.31		 not provided
NM_004664.2(LIN7A):c.121G>A (p.Glu41Lys) single nucleotide variant Malignant melanoma [RCV000070235] Chr12:80889331 [GRCh38]
Chr12:81283110 [GRCh37]
Chr12:79807241 [NCBI36]
Chr12:12q21.31		 not provided
NM_004664.2(LIN7A):c.155C>T (p.Ser52Phe) single nucleotide variant Malignant melanoma [RCV000062611] Chr12:80889297 [GRCh38]
Chr12:81283076 [GRCh37]
Chr12:79807207 [NCBI36]
Chr12:12q21.31		 not provided
NM_004664.2(LIN7A):c.83-6578A>T single nucleotide variant Lung cancer [RCV000111347] Chr12:80895947 [GRCh38]
Chr12:81289726 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.2(LIN7A):c.202-7701G>T single nucleotide variant Lung cancer [RCV000111346] Chr12:80856023 [GRCh38]
Chr12:81249802 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.274-4del deletion not specified [RCV000202744] Chr12:80845943 [GRCh38]
Chr12:81239722 [GRCh37]
Chr12:12q21.31		 benign
GRCh38/hg38 12q21.31(chr12:80752724-80856919)x1 copy number loss See cases [RCV000137283] Chr12:80752724..80856919 [GRCh38]
Chr12:81146503..81250698 [GRCh37]
Chr12:79670634..79774829 [NCBI36]
Chr12:12q21.31		 likely benign
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12q21.2-21.31(chr12:76566873-82021089)x1 copy number loss See cases [RCV000141023] Chr12:76566873..82021089 [GRCh38]
Chr12:76960653..82414868 [GRCh37]
Chr12:75484784..80938999 [NCBI36]
Chr12:12q21.2-21.31		 likely pathogenic
GRCh38/hg38 12q21.1-22(chr12:73485697-92795805)x1 copy number loss See cases [RCV000143099] Chr12:73485697..92795805 [GRCh38]
Chr12:73879477..93189581 [GRCh37]
Chr12:72165744..91713712 [NCBI36]
Chr12:12q21.1-22		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic|likely pathogenic
GRCh37/hg19 12q21.31(chr12:80927874-81503412)x3 copy number gain Breast ductal adenocarcinoma [RCV000207319] Chr12:80927874..81503412 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12q21.31(chr12:80902982-81207393)x1 copy number loss See cases [RCV000447661] Chr12:80902982..81207393 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12q21.31(chr12:80622857-81449637)x3 copy number gain See cases [RCV000512357] Chr12:80622857..81449637 [GRCh37]
Chr12:12q21.31		 uncertain significance
t(12;14)(q14;q13)dn translocation not provided [RCV000714247] Chr12:81201999 [GRCh37]
Chr14:33850610..33850620 [GRCh37]
Chr12:12q21.31
Chr14:14q13.1		 likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12q15-21.33(chr12:69608090-89629345)x1 copy number loss not provided [RCV000737927] Chr12:69608090..89629345 [GRCh37]
Chr12:12q15-21.33		 pathogenic
NM_004664.4(LIN7A):c.567C>A (p.Thr189=) single nucleotide variant not provided [RCV000964215] Chr12:80811600 [GRCh38]
Chr12:81205379 [GRCh37]
Chr12:12q21.31		 benign
GRCh37/hg19 12q21.31(chr12:81327644-82029969)x1 copy number loss not provided [RCV000849716] Chr12:81327644..82029969 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12q21.31(chr12:81197619-81306996)x3 copy number gain not provided [RCV000847111] Chr12:81197619..81306996 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12q21.31(chr12:81179432-81274967)x3 copy number gain not provided [RCV000847893] Chr12:81179432..81274967 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12q21.2-22(chr12:77737623-94330526)x1 copy number loss not provided [RCV000848027] Chr12:77737623..94330526 [GRCh37]
Chr12:12q21.2-22		 pathogenic
GRCh37/hg19 12q21.2-21.31(chr12:79302790-82128250)x1 copy number loss not provided [RCV001006516] Chr12:79302790..82128250 [GRCh37]
Chr12:12q21.2-21.31		 uncertain significance
GRCh37/hg19 12q21.31(chr12:80902982-81207393) copy number loss not specified [RCV002053003] Chr12:80902982..81207393 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.400A>G (p.Ile134Val) single nucleotide variant Inborn genetic diseases [RCV002778461] Chr12:80845813 [GRCh38]
Chr12:81239592 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.339G>T (p.Lys113Asn) single nucleotide variant Inborn genetic diseases [RCV002754629] Chr12:80845874 [GRCh38]
Chr12:81239653 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.428C>T (p.Ala143Val) single nucleotide variant Inborn genetic diseases [RCV002879206] Chr12:80845785 [GRCh38]
Chr12:81239564 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.58G>A (p.Val20Ile) single nucleotide variant Inborn genetic diseases [RCV002655955] Chr12:80937665 [GRCh38]
Chr12:81331444 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.415C>T (p.Pro139Ser) single nucleotide variant Inborn genetic diseases [RCV003188726] Chr12:80845798 [GRCh38]
Chr12:81239577 [GRCh37]
Chr12:12q21.31		 uncertain significance
NM_004664.4(LIN7A):c.651G>T (p.Gln217His) single nucleotide variant Inborn genetic diseases [RCV003367116] Chr12:80811516 [GRCh38]
Chr12:81205295 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12q21.31(chr12:80647969-85713707)x1 copy number loss not provided [RCV003483158] Chr12:80647969..85713707 [GRCh37]
Chr12:12q21.31		 uncertain significance
GRCh37/hg19 12q21.1-21.33(chr12:74887087-90469800)x1 copy number loss not specified [RCV003986972] Chr12:74887087..90469800 [GRCh37]
Chr12:12q21.1-21.33		 pathogenic
GRCh37/hg19 12q21.1-21.31(chr12:73466055-82398026)x1 copy number loss not specified [RCV003986983] Chr12:73466055..82398026 [GRCh37]
Chr12:12q21.1-21.31		 uncertain significance
GRCh37/hg19 12q21.31(chr12:80696867-81266911)x1 copy number loss not specified [RCV003986975] Chr12:80696867..81266911 [GRCh37]
Chr12:12q21.31		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2152
Count of miRNA genes:994
Interacting mature miRNAs:1214
Transcripts:ENST00000261203, ENST00000549417, ENST00000552093, ENST00000552864
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.

Markers in Region
RH66117  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,205,286 - 81,205,462UniSTSGRCh37
Build 361279,729,417 - 79,729,593RGDNCBI36
Celera1280,871,487 - 80,871,663RGD
Cytogenetic Map12q21UniSTS
HuRef1278,262,154 - 78,262,330UniSTS
GeneMap99-GB4 RH Map12349.54UniSTS
RH46592  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,237,888 - 81,238,010UniSTSGRCh37
Build 361279,762,019 - 79,762,141RGDNCBI36
Celera1280,904,059 - 80,904,181RGD
Cytogenetic Map12q21UniSTS
HuRef1278,294,747 - 78,294,869UniSTS
SHGC-81706  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,326,421 - 81,326,763UniSTSGRCh37
Build 361279,850,552 - 79,850,894RGDNCBI36
Celera1280,992,580 - 80,992,922RGD
Cytogenetic Map12q21UniSTS
HuRef1278,383,312 - 78,383,654UniSTS
TNG Radiation Hybrid Map1237527.0UniSTS
G60266  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,237,880 - 81,238,008UniSTSGRCh37
Build 361279,762,011 - 79,762,139RGDNCBI36
Celera1280,904,051 - 80,904,179RGD
Cytogenetic Map12q21UniSTS
HuRef1278,294,739 - 78,294,867UniSTS
TNG Radiation Hybrid Map1237490.0UniSTS
G62497  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,253,330 - 81,253,607UniSTSGRCh37
Build 361279,777,461 - 79,777,738RGDNCBI36
Celera1280,919,500 - 80,919,777RGD
Cytogenetic Map12q21UniSTS
HuRef1278,310,183 - 78,310,460UniSTS
TNG Radiation Hybrid Map1237479.0UniSTS
SHGC-142287  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,306,594 - 81,306,887UniSTSGRCh37
Build 361279,830,725 - 79,831,018RGDNCBI36
Celera1280,972,753 - 80,973,046RGD
Cytogenetic Map12q21UniSTS
HuRef1278,363,485 - 78,363,778UniSTS
TNG Radiation Hybrid Map1237511.0UniSTS
LIN7A_8861  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371281,190,975 - 81,191,501UniSTSGRCh37
Build 361279,715,106 - 79,715,632RGDNCBI36
Celera1280,857,190 - 80,857,716RGD
HuRef1278,247,858 - 78,248,384UniSTS
G64269  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12q21UniSTS


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
High
Medium 47 393 242 109 638 110 458 65 959 171 255 283 127 211
Low 2167 2549 1435 494 1084 345 3358 1905 2737 226 1055 1214 151 1076 2291 2
Below cutoff 150 38 44 18 95 6 518 220 31 15 105 67 15 1 1 286 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_050580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001324423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_004664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_136887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_136888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011538928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054373707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC025568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC068798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC078886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF028826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF087693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF173081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK022997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK309256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK315321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC041400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC046926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC062332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC118609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC122561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR407680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF495781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000261203   ⟹   ENSP00000261203
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1280,797,575 - 80,937,780 (-)Ensembl
RefSeq Acc Id: ENST00000549417   ⟹   ENSP00000448975
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1280,841,689 - 80,937,704 (-)Ensembl
RefSeq Acc Id: ENST00000552093   ⟹   ENSP00000448891
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1280,845,564 - 80,889,348 (-)Ensembl
RefSeq Acc Id: ENST00000552864   ⟹   ENSP00000447488
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1280,792,520 - 80,937,934 (-)Ensembl
RefSeq Acc Id: NM_001324423   ⟹   NP_001311352
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,792,520 - 80,937,707 (-)NCBI
CHM1_11281,152,694 - 81,298,106 (-)NCBI
T2T-CHM13v2.01280,771,214 - 80,916,550 (-)NCBI
Sequence:
RefSeq Acc Id: NM_004664   ⟹   NP_004655
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,792,520 - 80,937,934 (-)NCBI
GRCh371281,191,171 - 81,331,702 (-)NCBI
Build 361279,715,302 - 79,855,825 (-)NCBI Archive
HuRef1278,248,054 - 78,388,586 (-)ENTREZGENE
CHM1_11281,152,694 - 81,298,106 (-)NCBI
T2T-CHM13v2.01280,771,214 - 80,916,777 (-)NCBI
Sequence:
RefSeq Acc Id: NR_136887
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,792,520 - 80,937,707 (-)NCBI
CHM1_11281,152,694 - 81,298,106 (-)NCBI
T2T-CHM13v2.01280,771,214 - 80,916,550 (-)NCBI
Sequence:
RefSeq Acc Id: NR_136888
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,792,520 - 80,937,934 (-)NCBI
CHM1_11281,152,694 - 81,298,106 (-)NCBI
T2T-CHM13v2.01280,771,214 - 80,916,777 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011538928   ⟹   XP_011537230
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,792,520 - 80,937,934 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054373707   ⟹   XP_054229682
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01280,771,214 - 80,916,777 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_004655   ⟸   NM_004664
- Peptide Label: isoform 1
- UniProtKB: Q6LES3 (UniProtKB/Swiss-Prot),   Q147W1 (UniProtKB/Swiss-Prot),   A4FTY3 (UniProtKB/Swiss-Prot),   Q7LDS4 (UniProtKB/Swiss-Prot),   O14910 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011537230   ⟸   XM_011538928
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001311352   ⟸   NM_001324423
- Peptide Label: isoform 2
- Sequence:
RefSeq Acc Id: ENSP00000448975   ⟸   ENST00000549417
RefSeq Acc Id: ENSP00000261203   ⟸   ENST00000261203
RefSeq Acc Id: ENSP00000448891   ⟸   ENST00000552093
RefSeq Acc Id: ENSP00000447488   ⟸   ENST00000552864
RefSeq Acc Id: XP_054229682   ⟸   XM_054373707
- Peptide Label: isoform X1
Protein Domains
L27   PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O14910-F1-model_v2 AlphaFold O14910 1-233 view protein structure

Promoters
RGD ID:6790207
Promoter ID:HG_KWN:16238
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid,   NB4
Transcripts:NM_004664,   UC001SZK.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361279,855,521 - 79,856,452 (-)MPROMDB
RGD ID:7224909
Promoter ID:EPDNEW_H18200
Type:initiation region
Name:LIN7A_1
Description:lin-7 homolog A, crumbs cell polarity complex component
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H18201  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,937,707 - 80,937,767EPDNEW
RGD ID:7224911
Promoter ID:EPDNEW_H18201
Type:initiation region
Name:LIN7A_2
Description:lin-7 homolog A, crumbs cell polarity complex component
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H18200  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381280,937,934 - 80,937,994EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17787 AgrOrtholog
COSMIC LIN7A COSMIC
Ensembl Genes ENSG00000111052 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000261203.7 UniProtKB/TrEMBL
  ENST00000549417.5 UniProtKB/TrEMBL
  ENST00000552093.1 UniProtKB/TrEMBL
  ENST00000552864 ENTREZGENE
  ENST00000552864.6 UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L27 domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000111052 GTEx
HGNC ID HGNC:17787 ENTREZGENE
Human Proteome Map LIN7A Human Proteome Map
InterPro L27_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L27_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L27_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIN7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8825 UniProtKB/Swiss-Prot
NCBI Gene 8825 ENTREZGENE
OMIM 603380 OMIM
PANTHER PROTEIN LIN-7 HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN LIN-7 HOMOLOG A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam L27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134881936 PharmGKB
PIRSF Lin-7_homologue UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE L27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART L27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF101288 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A4FTY3 ENTREZGENE
  H0YI92_HUMAN UniProtKB/TrEMBL
  H0YIA8_HUMAN UniProtKB/TrEMBL
  J3KN23_HUMAN UniProtKB/TrEMBL
  LIN7A_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q147W1 ENTREZGENE
  Q6LES3 ENTREZGENE
  Q7LDS4 ENTREZGENE
UniProt Secondary A4FTY3 UniProtKB/Swiss-Prot
  Q147W1 UniProtKB/Swiss-Prot
  Q6LES3 UniProtKB/Swiss-Prot
  Q7LDS4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-29 LIN7A  lin-7 homolog A, crumbs cell polarity complex component    lin-7 homolog A (C. elegans)  Symbol and/or name change 5135510 APPROVED