LCN9 (lipocalin 9) - Rat Genome Database

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Gene: LCN9 (lipocalin 9) Homo sapiens
Analyze
Symbol: LCN9
Name: lipocalin 9
RGD ID: 1345733
HGNC Page HGNC:17442
Description: Predicted to enable small molecule binding activity. Predicted to be located in extracellular region. Predicted to be active in extracellular space.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 9230102I19Rik; epididymal-specific lipocalin-9; epididymis luminal protein 129; HEL129; MUP-like lipocalin
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,663,309 - 135,666,961 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,663,309 - 135,666,961 (+)EnsemblGRCh38hg38GRCh38
GRCh379138,555,155 - 138,558,807 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,694,989 - 137,697,770 (+)NCBINCBI36Build 36hg18NCBI36
Build 349135,781,112 - 135,783,700NCBI
Celera9109,072,999 - 109,075,781 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,017,019 - 108,019,760 (+)NCBIHuRef
CHM1_19138,703,687 - 138,706,468 (+)NCBICHM1_1
T2T-CHM13v2.09147,889,683 - 147,893,335 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15164053   PMID:15363845   PMID:21873635   PMID:32296183   PMID:33961781  


Genomics

Comparative Map Data
LCN9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,663,309 - 135,666,961 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,663,309 - 135,666,961 (+)EnsemblGRCh38hg38GRCh38
GRCh379138,555,155 - 138,558,807 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,694,989 - 137,697,770 (+)NCBINCBI36Build 36hg18NCBI36
Build 349135,781,112 - 135,783,700NCBI
Celera9109,072,999 - 109,075,781 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,017,019 - 108,019,760 (+)NCBIHuRef
CHM1_19138,703,687 - 138,706,468 (+)NCBICHM1_1
T2T-CHM13v2.09147,889,683 - 147,893,335 (+)NCBIT2T-CHM13v2.0
Lcn9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,713,100 - 25,715,558 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,713,165 - 25,715,549 (+)EnsemblGRCm39 Ensembl
GRCm38225,823,088 - 25,825,546 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,823,153 - 25,825,537 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,678,673 - 25,681,057 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,645,162 - 25,647,546 (+)NCBIMGSCv36mm8
Celera225,542,705 - 25,545,089 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.15NCBI
Lcn9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,041,710 - 29,050,677 (+)NCBIGRCr8
mRatBN7.238,644,427 - 8,646,782 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,636,548 - 8,652,200 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,698,621 - 11,700,973 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,281,832 - 20,284,184 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,537,153 - 18,539,505 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,272,150 - 3,274,792 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,272,193 - 3,274,547 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.038,634,275 - 8,636,629 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,996,496 - 3,998,850 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,996,506 - 3,998,233 (+)NCBI
Celera33,467,437 - 3,469,791 (+)NCBICelera
Cytogenetic Map3p13NCBI
Lcn9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555134,786,615 - 4,788,768 (-)NCBIChiLan1.0ChiLan1.0
LCN9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2113,720,888 - 3,724,539 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan193,723,221 - 3,726,872 (-)NCBINHGRI_mPanPan1
LCN9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,632,813 - 49,636,854 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,632,799 - 49,637,517 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,885,218 - 48,889,279 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,511,967 - 50,516,033 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,513,262 - 50,515,241 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,291,922 - 49,295,114 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,586,426 - 49,590,488 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,635,077 - 49,638,824 (-)NCBIUU_Cfam_GSD_1.0
Lcn9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,443,005 - 201,444,836 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366691,930,222 - 1,932,053 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCN9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21308,696,220 - 308,698,468 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCN9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1122,526,003 - 2,530,175 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660582,631,001 - 2,634,529 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lcn9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247601,143,457 - 1,145,561 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LCN9
8 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121112395-138075224)x3 copy number gain See cases [RCV000051009] Chr9:121112395..138075224 [GRCh38]
Chr9:123874673..140969676 [GRCh37]
Chr9:122914494..140089497 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:122792658-138124532)x3 copy number gain See cases [RCV000051040] Chr9:122792658..138124532 [GRCh38]
Chr9:125554937..141018984 [GRCh37]
Chr9:124594758..140138805 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134428674-138154922)x1 copy number loss See cases [RCV000052936] Chr9:134428674..138154922 [GRCh38]
Chr9:137320520..141049374 [GRCh37]
Chr9:136460341..140169195 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135452016-137613738)x1 copy number loss See cases [RCV000052937] Chr9:135452016..137613738 [GRCh38]
Chr9:138343862..140508190 [GRCh37]
Chr9:137483683..139628011 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:129068560-136495351)x3 copy number gain See cases [RCV000053779] Chr9:129068560..136495351 [GRCh38]
Chr9:131830839..139389803 [GRCh37]
Chr9:130870660..138509624 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|See cases [RCV000053748] Chr9:193412..138179445 [GRCh38]
Chr9:266045..141073897 [GRCh37]
Chr9:256045..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134174698-138138735)x3 copy number gain See cases [RCV000053814] Chr9:134174698..138138735 [GRCh38]
Chr9:137091194..141033187 [GRCh37]
Chr9:136029641..140153008 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121586837-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053776]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053776]|See cases [RCV000053776] Chr9:121586837..138179445 [GRCh38]
Chr9:124349116..141073897 [GRCh37]
Chr9:123388937..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:130513207-138124532)x3 copy number gain See cases [RCV000133778] Chr9:130513207..138124532 [GRCh38]
Chr9:133388594..141018984 [GRCh37]
Chr9:132378415..140138805 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135164984-136437047)x3 copy number gain See cases [RCV000134910] Chr9:135164984..136437047 [GRCh38]
Chr9:138056830..139331499 [GRCh37]
Chr9:137196651..138451320 [NCBI36]
Chr9:9q34.3		 uncertain significance
GRCh38/hg38 9q34.11-34.3(chr9:129068560-138179445)x3 copy number gain See cases [RCV000134916] Chr9:129068560..138179445 [GRCh38]
Chr9:131830839..141073897 [GRCh37]
Chr9:130870660..140193718 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121073102-138179445)x3 copy number gain See cases [RCV000134920] Chr9:121073102..138179445 [GRCh38]
Chr9:123835380..141073897 [GRCh37]
Chr9:122875201..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 copy number gain See cases [RCV000136790] Chr9:132986903..138114463 [GRCh38]
Chr9:135862290..141008915 [GRCh37]
Chr9:134852111..140128736 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133504071-138159073)x3 copy number gain See cases [RCV000137825] Chr9:133504071..138159073 [GRCh38]
Chr9:136324358..141053525 [GRCh37]
Chr9:135314179..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133996227-138124524)x3 copy number gain See cases [RCV000139807] Chr9:133996227..138124524 [GRCh38]
Chr9:136861349..141018976 [GRCh37]
Chr9:135851170..140138797 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133918071-138159073)x3 copy number gain See cases [RCV000142955] Chr9:133918071..138159073 [GRCh38]
Chr9:136783193..141053525 [GRCh37]
Chr9:135773014..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132386553-138059695)x3 copy number gain See cases [RCV000142636] Chr9:132386553..138059695 [GRCh38]
Chr9:135261940..140954147 [GRCh37]
Chr9:134251761..140073968 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135665886-135775364)x1 copy number loss Breast ductal adenocarcinoma [RCV000207248] Chr9:135665886..135775364 [GRCh38]
Chr9:138557731..138667209 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9p24.3-q34.3(chr9:163131-141122114)x3 copy number gain See cases [RCV000240081] Chr9:163131..141122114 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:62525-141006407) copy number gain See cases [RCV000449375] Chr9:62525..141006407 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138222049-141018925)x1 copy number loss See cases [RCV000446074] Chr9:138222049..141018925 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203861-141020389)x3 copy number gain not specified [RCV003986800] Chr9:203861..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q33.3-34.3(chr9:128652785-141044751)x3 copy number gain See cases [RCV000447080] Chr9:128652785..141044751 [GRCh37]
Chr9:9q33.3-34.3		 pathogenic
GRCh37/hg19 9q33.2-34.3(chr9:124642754-141146461)x3 copy number gain See cases [RCV000448784] Chr9:124642754..141146461 [GRCh37]
Chr9:9q33.2-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138222049-138711104)x3 copy number gain See cases [RCV000448897] Chr9:138222049..138711104 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9p24.3-q34.3(chr9:203864-141020389)x3 copy number gain See cases [RCV000448978] Chr9:203864..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138209358-141020389)x1 copy number loss See cases [RCV000510584] Chr9:138209358..141020389 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138275621-141020389)x3 copy number gain See cases [RCV000511188] Chr9:138275621..141020389 [GRCh37]
Chr9:9q34.3		 likely pathogenic
GRCh37/hg19 9q21.11-34.3(chr9:71069743-140999928) copy number gain Global developmental delay [RCV000626548] Chr9:71069743..140999928 [GRCh37]
Chr9:9q21.11-34.3		 likely pathogenic
GRCh37/hg19 9q34.13-34.3(chr9:135377559-141213431)x1 copy number loss mTOR Inhibitor response [RCV000626442] Chr9:135377559..141213431 [GRCh37]
Chr9:9q34.13-34.3		 drug response
NM_001393661.1(LCN9):c.44C>T (p.Ala15Val) single nucleotide variant not specified [RCV004296866] Chr9:135663365 [GRCh38]
Chr9:138555211 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9p24.3-q34.3(chr9:203862-141020389) copy number gain See cases [RCV000512392] Chr9:203862..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:137736478-138563159)x3 copy number gain not provided [RCV000683146] Chr9:137736478..138563159 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q34.13-34.3(chr9:135105971-141020389)x3 copy number gain not provided [RCV000683160] Chr9:135105971..141020389 [GRCh37]
Chr9:9q34.13-34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141122247)x3 copy number gain not provided [RCV000748055] Chr9:10590..141122247 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:137816459-141114095)x1 copy number loss not provided [RCV000748787] Chr9:137816459..141114095 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141107672)x3 copy number gain not provided [RCV000748053] Chr9:10590..141107672 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:46587-141066491)x3 copy number gain not provided [RCV000748063] Chr9:46587..141066491 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141114095)x2 copy number gain not provided [RCV000748054] Chr9:10590..141114095 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203861-141020388)x3 copy number gain not provided [RCV000845900] Chr9:203861..141020388 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
NC_000009.11:g.(?_134379574)_(138678377_?)dup duplication Ehlers-Danlos syndrome, classic type [RCV000807925] Chr9:134379574..138678377 [GRCh37]
Chr9:9q34.13-34.3		 uncertain significance
GRCh37/hg19 9q21.11-34.3(chr9:71416475-141020389)x3 copy number gain not provided [RCV000847808] Chr9:71416475..141020389 [GRCh37]
Chr9:9q21.11-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:137880493-138781516)x3 copy number gain See cases [RCV001194592] Chr9:137880493..138781516 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q34.3(chr9:138225001-141015001) copy number loss Microcephaly [RCV001252947] Chr9:138225001..141015001 [GRCh37]
Chr9:9q34.3		 pathogenic
NC_000009.11:g.(?_137534034)_(139440238_?)dup duplication Adams-Oliver syndrome 5 [RCV003120731]|Ehlers-Danlos syndrome, classic type, 1 [RCV001872736] Chr9:137534034..139440238 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9p24.3-q34.3(chr9:353349-141020389) copy number gain not specified [RCV002053823] Chr9:353349..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
NC_000009.11:g.(?_135139626)_(140034216_?)dup duplication Developmental and epileptic encephalopathy, 14 [RCV003111109]|Leigh syndrome [RCV003122287]|Rafiq syndrome [RCV003122286]|Tuberous sclerosis 1 [RCV003111108] Chr9:135139626..140034216 [GRCh37]
Chr9:9q34.13-34.3		 uncertain significance
NC_000009.11:g.(?_138392557)_(141016451_?)del deletion Adams-Oliver syndrome 5 [RCV003119767]|Developmental and epileptic encephalopathy, 14 [RCV003109684]|Familial aplasia of the vermis [RCV003119768] Chr9:138392557..141016451 [GRCh37]
Chr9:9q34.3		 pathogenic|uncertain significance
NC_000009.11:g.(?_131087402)_(141016451_?)dup duplication Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome [RCV003119700] Chr9:131087402..141016451 [GRCh37]
Chr9:9q34.11-34.3		 uncertain significance
NC_000009.11:g.(?_136218768)_(141016451_?)dup duplication Kleefstra syndrome 1 [RCV003122719] Chr9:136218768..141016451 [GRCh37]
Chr9:9q34.2-34.3		 uncertain significance
NM_001393661.1(LCN9):c.404C>A (p.Thr135Lys) single nucleotide variant not specified [RCV004104642] Chr9:135665341 [GRCh38]
Chr9:138557187 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.262G>A (p.Val88Met) single nucleotide variant not specified [RCV004230049] Chr9:135664750 [GRCh38]
Chr9:138556596 [GRCh37]
Chr9:9q34.3		 likely benign
GRCh38/hg38 9q34.3(chr9:134962336-137240181)x1 copy number loss See cases [RCV002640756] Chr9:134962336..137240181 [GRCh38]
Chr9:9q34.3		 pathogenic
NM_001393661.1(LCN9):c.26G>A (p.Gly9Glu) single nucleotide variant not specified [RCV004171314] Chr9:135663347 [GRCh38]
Chr9:138555193 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.51G>T (p.Glu17Asp) single nucleotide variant not specified [RCV004129654] Chr9:135663372 [GRCh38]
Chr9:138555218 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.146G>C (p.Arg49Pro) single nucleotide variant not specified [RCV004257201] Chr9:135664211 [GRCh38]
Chr9:138556057 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.40G>A (p.Ala14Thr) single nucleotide variant not specified [RCV004327907] Chr9:135663361 [GRCh38]
Chr9:138555207 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.253G>A (p.Ala85Thr) single nucleotide variant not specified [RCV004341012] Chr9:135664741 [GRCh38]
Chr9:138556587 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q34.2-34.3(chr9:136988996-141020389)x3 copy number gain not provided [RCV003484786] Chr9:136988996..141020389 [GRCh37]
Chr9:9q34.2-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:137892345-138866686)x3 copy number gain not specified [RCV003986834] Chr9:137892345..138866686 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.125T>C (p.Met42Thr) single nucleotide variant not specified [RCV004412518] Chr9:135664190 [GRCh38]
Chr9:138556036 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.182G>A (p.Arg61Gln) single nucleotide variant not specified [RCV004412519] Chr9:135664247 [GRCh38]
Chr9:138556093 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.235G>A (p.Val79Met) single nucleotide variant not specified [RCV004412520] Chr9:135664723 [GRCh38]
Chr9:138556569 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_001393661.1(LCN9):c.43G>T (p.Ala15Ser) single nucleotide variant not specified [RCV004412521] Chr9:135663364 [GRCh38]
Chr9:138555210 [GRCh37]
Chr9:9q34.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:909
Count of miRNA genes:603
Interacting mature miRNAs:693
Transcripts:ENST00000277526, ENST00000430290, ENST00000554343
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
RH104568  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh379138,556,605 - 138,558,220UniSTSGRCh37
Celera9109,074,437 - 109,076,052UniSTS
Cytogenetic Map9q34.3UniSTS
HuRef9108,018,416 - 108,020,031UniSTS
GeneMap99-GB4 RH Map1538.38UniSTS


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 3 3 1 2 1
Low 8 4 95 14 86 7 368 1 99 52 17 10
Below cutoff 336 282 346 22 131 12 646 243 1871 21 473 319 10 239 403 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000277526   ⟹   ENSP00000277526
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,663,309 - 135,666,959 (+)Ensembl
RefSeq Acc Id: ENST00000430290
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,663,336 - 135,665,908 (+)Ensembl
RefSeq Acc Id: ENST00000554343
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,665,222 - 135,666,422 (+)Ensembl
RefSeq Acc Id: ENST00000619315   ⟹   ENSP00000482296
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,663,309 - 135,666,961 (+)Ensembl
RefSeq Acc Id: NM_001393661   ⟹   NP_001380590
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,663,309 - 135,666,961 (+)NCBI
T2T-CHM13v2.09147,889,683 - 147,893,335 (+)NCBI
Sequence:
RefSeq Acc Id: NR_171893
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,663,309 - 135,666,961 (+)NCBI
T2T-CHM13v2.09147,889,683 - 147,893,335 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001380590 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ81975 (Get FASTA)   NCBI Sequence Viewer  
  ACJ13733 (Get FASTA)   NCBI Sequence Viewer  
  CAD32055 (Get FASTA)   NCBI Sequence Viewer  
  EAW88172 (Get FASTA)   NCBI Sequence Viewer  
  EAW88173 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000277526.4
  ENSP00000482296
  ENSP00000482296.2
GenBank Protein Q8WX39 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSP00000482296   ⟸   ENST00000619315
RefSeq Acc Id: ENSP00000277526   ⟸   ENST00000277526
RefSeq Acc Id: NP_001380590   ⟸   NM_001393661
- Peptide Label: precursor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8WX39-F1-model_v2 AlphaFold Q8WX39 1-176 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17442 AgrOrtholog
COSMIC LCN9 COSMIC
Ensembl Genes ENSG00000148386 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000277526 ENTREZGENE
  ENST00000277526.8 UniProtKB/TrEMBL
  ENST00000619315 ENTREZGENE
  ENST00000619315.2 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot
GTEx ENSG00000148386 GTEx
HGNC ID HGNC:17442 ENTREZGENE
Human Proteome Map LCN9 Human Proteome Map
InterPro Calycin UniProtKB/Swiss-Prot
  Lipocalin UniProtKB/Swiss-Prot
  Lipocalin_CS UniProtKB/Swiss-Prot
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot
  Maj_urinary UniProtKB/Swiss-Prot
NCBI Gene 392399 ENTREZGENE
OMIM 612903 OMIM
PANTHER EPIDIDYMAL-SPECIFIC LIPOCALIN-9 UniProtKB/Swiss-Prot
  PTHR11430 UniProtKB/Swiss-Prot
Pfam Lipocalin UniProtKB/Swiss-Prot
PharmGKB PA134879860 PharmGKB
PRINTS MAJORURINARY UniProtKB/Swiss-Prot
PROSITE LIPOCALIN UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot
UniProt A0AAA9WZE8_HUMAN UniProtKB/TrEMBL
  LCN9_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A0A087WZ21 UniProtKB/Swiss-Prot
  C9J5F0 UniProtKB/Swiss-Prot
  Q6JVE7 UniProtKB/Swiss-Prot