LCN1 (lipocalin 1) - Rat Genome Database

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Gene: LCN1 (lipocalin 1) Homo sapiens
Analyze
Symbol: LCN1
Name: lipocalin 1
RGD ID: 1344178
HGNC Page HGNC:6525
Description: Enables chloride ion binding activity; signaling receptor binding activity; and zinc ion binding activity. Predicted to be involved in proteolysis. Located in extracellular space.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: lipocalin 1 (tear prealbumin); lipocalin 1-like 2; lipocalin-1; MGC71975; PMFA; protein migrating faster than albumin; tear lipocalin; tear prealbumin; TLC; TP; VEG protein; VEGP; Von Ebner gland protein
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Related Pseudogenes: LCN1P1   LCN1P2  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,521,440 - 135,526,540 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,521,438 - 135,526,540 (+)EnsemblGRCh38hg38GRCh38
GRCh379138,413,286 - 138,418,386 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,553,107 - 137,558,199 (+)NCBINCBI36Build 36hg18NCBI36
Build 349135,639,230 - 135,644,323NCBI
Celera9108,930,399 - 108,935,455 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9107,875,074 - 107,880,176 (+)NCBIHuRef
CHM1_19138,561,863 - 138,566,965 (+)NCBICHM1_1
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
extracellular region  (IEA,TAS)
extracellular space  (HDA,IBA,IDA)

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:1400345   PMID:7606920   PMID:7679926   PMID:8112601   PMID:8276406   PMID:8500570   PMID:8898072   PMID:8999869   PMID:9759656   PMID:10558865   PMID:11287427   PMID:11727836  
PMID:11850445   PMID:12477932   PMID:12591932   PMID:12613960   PMID:12613961   PMID:12613963   PMID:15461462   PMID:15489334   PMID:15489503   PMID:15851553   PMID:16249071   PMID:17353931  
PMID:17869594   PMID:17945179   PMID:18334931   PMID:19586017   PMID:19770509   PMID:20360068   PMID:21324447   PMID:21466861   PMID:21791187   PMID:21805676   PMID:21873635   PMID:22664934  
PMID:23376485   PMID:23580065   PMID:23686814   PMID:24550385   PMID:24920892   PMID:24981860   PMID:25914748   PMID:25921289   PMID:26135974   PMID:26186194   PMID:26218644   PMID:26366224  
PMID:26485645   PMID:27591049   PMID:28514442   PMID:28685749   PMID:28977666   PMID:29331331   PMID:29426014   PMID:29509190   PMID:30884312   PMID:31059266   PMID:31180492   PMID:31300519  
PMID:31409639   PMID:31424267   PMID:31436131   PMID:31992359   PMID:32235678   PMID:32296183   PMID:32707033   PMID:33631671   PMID:33961781   PMID:34445801   PMID:34795231   PMID:34943047  
PMID:35338135   PMID:35831895   PMID:35833506   PMID:35864588   PMID:35945219   PMID:35995384   PMID:36225252   PMID:36273042   PMID:36307841   PMID:36964488   PMID:37314216   PMID:39147351  


Genomics

Comparative Map Data
LCN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,521,440 - 135,526,540 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,521,438 - 135,526,540 (+)EnsemblGRCh38hg38GRCh38
GRCh379138,413,286 - 138,418,386 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,553,107 - 137,558,199 (+)NCBINCBI36Build 36hg18NCBI36
Build 349135,639,230 - 135,644,323NCBI
Celera9108,930,399 - 108,935,455 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9107,875,074 - 107,880,176 (+)NCBIHuRef
CHM1_19138,561,863 - 138,566,965 (+)NCBICHM1_1
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBIT2T-CHM13v2.0
Lcn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,655,545 - 25,658,110 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,655,581 - 25,658,111 (+)EnsemblGRCm39 Ensembl
GRCm38225,765,533 - 25,768,098 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,765,569 - 25,768,099 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,621,089 - 25,623,619 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,587,578 - 25,590,108 (+)NCBIMGSCv36mm8
Celera225,491,663 - 25,494,194 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.99NCBI
Lcn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,930,943 - 29,935,418 (+)NCBIGRCr8
mRatBN7.239,532,860 - 9,537,859 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,532,915 - 9,536,577 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx312,590,063 - 12,594,538 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,175,443 - 21,179,918 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0319,430,763 - 19,435,238 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.034,233,111 - 4,236,960 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl34,233,111 - 4,236,960 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.039,591,615 - 9,595,715 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,879,048 - 4,883,523 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.134,879,047 - 4,883,523 (+)NCBI
Celera34,345,110 - 4,349,585 (+)NCBICelera
Cytogenetic Map3p13NCBI
LCN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2113,790,985 - 3,796,299 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan193,793,318 - 3,798,632 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09106,662,265 - 106,667,575 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19135,654,722 - 135,659,870 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9135,654,722 - 135,659,869 (+)Ensemblpanpan1.1panPan2
OBP2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,707,505 - 49,709,999 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,706,531 - 49,710,097 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,959,918 - 48,962,412 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,579,508 - 50,582,002 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,578,536 - 50,582,050 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,341,983 - 49,344,477 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,656,392 - 49,658,886 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,706,778 - 49,709,273 (-)NCBIUU_Cfam_GSD_1.0
Lcn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,374,686 - 201,380,152 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366691,996,399 - 2,000,130 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OBP2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11272,886,871 - 272,890,537 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LCN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1122,639,012 - 2,648,767 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl122,640,102 - 2,648,073 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660582,509,481 - 2,515,221 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in LCN1
17 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(chr9:122792658-138124532)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 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 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 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 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(chr9:193412-138179445)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 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 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 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 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 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
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 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 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(chr9:138209358-141020389)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 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
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 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
NM_002297.4(LCN1):c.297G>A (p.Gly99=) single nucleotide variant not provided [RCV000883056] Chr9:135523884 [GRCh38]
Chr9:138415730 [GRCh37]
Chr9:9q34.3		 benign
NM_002297.4(LCN1):c.298G>C (p.Gly100Arg) single nucleotide variant not provided [RCV000883057] Chr9:135523885 [GRCh38]
Chr9:138415731 [GRCh37]
Chr9:9q34.3		 benign
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 9q34.3(chr9:138023579-138498904)x3 copy number gain not provided [RCV001006280] Chr9:138023579..138498904 [GRCh37]
Chr9:9q34.3		 uncertain significance
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 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(chr9:138225001-141015001) copy number loss Microcephaly [RCV001252947] Chr9:138225001..141015001 [GRCh37]
Chr9:9q34.3		 pathogenic
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.(?_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
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_002297.4(LCN1):c.463C>T (p.Arg155Cys) single nucleotide variant not specified [RCV004320938] Chr9:135524889 [GRCh38]
Chr9:138416735 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.233G>A (p.Arg78Gln) single nucleotide variant not specified [RCV004085054] Chr9:135523243 [GRCh38]
Chr9:138415089 [GRCh37]
Chr9:9q34.3		 likely benign
NM_002297.4(LCN1):c.526G>A (p.Asp176Asn) single nucleotide variant not specified [RCV004165482] Chr9:135525152 [GRCh38]
Chr9:138416998 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.499C>G (p.Gln167Glu) single nucleotide variant not specified [RCV004229955] Chr9:135524925 [GRCh38]
Chr9:138416771 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.454G>A (p.Ala152Thr) single nucleotide variant not specified [RCV004186511] Chr9:135524880 [GRCh38]
Chr9:138416726 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh38/hg38 9q34.3(chr9:134962336-137240181)x1 copy number loss See cases [RCV002640756] Chr9:134962336..137240181 [GRCh38]
Chr9:9q34.3		 pathogenic
NM_002297.4(LCN1):c.464G>A (p.Arg155His) single nucleotide variant not specified [RCV004187904] Chr9:135524890 [GRCh38]
Chr9:138416736 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.415A>G (p.Lys139Glu) single nucleotide variant not specified [RCV004272834] Chr9:135524841 [GRCh38]
Chr9:138416687 [GRCh37]
Chr9:9q34.3		 likely benign
NM_002297.4(LCN1):c.400G>A (p.Val134Met) single nucleotide variant not specified [RCV004348115] Chr9:135523987 [GRCh38]
Chr9:138415833 [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
NM_002297.4(LCN1):c.162G>A (p.Val54=) single nucleotide variant not provided [RCV003425857] Chr9:135522118 [GRCh38]
Chr9:138413964 [GRCh37]
Chr9:9q34.3		 likely benign
GRCh37/hg19 9q34.3(chr9:137892345-138866686)x3 copy number gain not specified [RCV003986834] Chr9:137892345..138866686 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh38/hg38 9q34.13-34.3(chr9:137590213-138052188) copy number loss Kleefstra syndrome 1 [RCV004720477] Chr9:137590213..138052188 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:137590213-137817525) copy number loss Kleefstra syndrome 1 [RCV004720478] Chr9:137590213..137817525 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:137552409-137879159) copy number loss Kleefstra syndrome 1 [RCV004720487] Chr9:137552409..137879159 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
NM_002297.4(LCN1):c.122C>T (p.Thr41Met) single nucleotide variant not specified [RCV004412486] Chr9:135522078 [GRCh38]
Chr9:138413924 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.184C>G (p.Leu62Val) single nucleotide variant not specified [RCV004412487] Chr9:135522140 [GRCh38]
Chr9:138413986 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.185T>A (p.Leu62Gln) single nucleotide variant not specified [RCV004412488] Chr9:135522141 [GRCh38]
Chr9:138413987 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.187G>C (p.Glu63Gln) single nucleotide variant not specified [RCV004412490] Chr9:135522143 [GRCh38]
Chr9:138413989 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.331G>T (p.Val111Leu) single nucleotide variant not specified [RCV004412491] Chr9:135523918 [GRCh38]
Chr9:138415764 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.370C>T (p.His124Tyr) single nucleotide variant not specified [RCV004412492] Chr9:135523957 [GRCh38]
Chr9:138415803 [GRCh37]
Chr9:9q34.3		 uncertain significance
NC_000009.11:g.(?_131678355)_(140095163_?)dup duplication not provided [RCV004582063] Chr9:131678355..140095163 [GRCh37]
Chr9:9q34.11-34.3		 uncertain significance
NM_002297.4(LCN1):c.287C>T (p.Thr96Met) single nucleotide variant not specified [RCV004642197] Chr9:135523297 [GRCh38]
Chr9:138415143 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.299G>A (p.Gly100Asp) single nucleotide variant not specified [RCV004642198] Chr9:135523886 [GRCh38]
Chr9:138415732 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_002297.4(LCN1):c.25A>T (p.Ser9Cys) single nucleotide variant not specified [RCV004642199] Chr9:135521522 [GRCh38]
Chr9:138413368 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh38/hg38 9q34.3(chr9:135182209-138129711) copy number loss Kleefstra syndrome 1 [RCV004720473] Chr9:135182209..138129711 [GRCh38]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:137552409-138059181) copy number loss Kleefstra syndrome 1 [RCV004720481] Chr9:137552409..138059181 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:134642187-138121999) copy number loss Kleefstra syndrome 1 [RCV004720503] Chr9:134642187..138121999 [GRCh38]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:136926151-138059181) copy number loss Kleefstra syndrome 1 [RCV004720480] Chr9:136926151..138059181 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134288333-138155727) copy number loss Kleefstra syndrome 1 [RCV004720515] Chr9:134288333..138155727 [GRCh38]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135203306-138100471) copy number loss Kleefstra syndrome 1 [RCV004720521] Chr9:135203306..138100471 [GRCh38]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135338745-138124196) copy number loss Kleefstra syndrome 1 [RCV004720539] Chr9:135338745..138124196 [GRCh38]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135008333-138199729) copy number loss Kleefstra syndrome 1 [RCV004720511] Chr9:135008333..138199729 [GRCh38]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:137552409-138052113) copy number loss Kleefstra syndrome 1 [RCV004720482] Chr9:137552409..138052113 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:137552082-137728529) copy number loss Kleefstra syndrome 1 [RCV004720485] Chr9:137552082..137728529 [GRCh38]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135204722-138394717) copy number loss Kleefstra syndrome 1 [RCV004720508] Chr9:135204722..138394717 [GRCh38]
Chr9:9q34.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:597
Count of miRNA genes:283
Interacting mature miRNAs:300
Transcripts:ENST00000263598, ENST00000371781
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
406905512GWAS554488_HS-6-hydroxywarfarin measurement QTL GWAS554488 (human)0.000005S-6-hydroxywarfarin measurement9135521597135521598Human

Markers in Region
RH66542  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh379138,416,749 - 138,418,280UniSTSGRCh37
Celera9108,933,826 - 108,935,357UniSTS
Cytogenetic Map9q34UniSTS
HuRef9107,878,539 - 107,880,070UniSTS
GeneMap99-GB4 RH Map9420.14UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
201 426 486 811 2427 499 678 1 110 406 68 453 1823 1628 22 2123 205 965 553 45 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001252617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001252618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001252619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_002297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011518675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047423375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054362961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054362962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL161452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL772161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC065721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC074925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC074926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD721968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK429694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK430667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK431106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L14927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M90424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X62418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X67647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000263598   ⟹   ENSP00000263598
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,521,438 - 135,526,532 (+)Ensembl
Ensembl Acc Id: ENST00000371781   ⟹   ENSP00000360846
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,521,440 - 135,526,540 (+)Ensembl
RefSeq Acc Id: NM_001252617   ⟹   NP_001239546
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,521,440 - 135,526,540 (+)NCBI
GRCh379138,413,284 - 138,418,386 (+)NCBI
HuRef9107,875,074 - 107,880,176 (+)NCBI
CHM1_19138,561,863 - 138,566,965 (+)NCBI
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001252618   ⟹   NP_001239547
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,521,440 - 135,526,540 (+)NCBI
GRCh379138,413,284 - 138,418,386 (+)NCBI
HuRef9107,875,074 - 107,880,176 (+)NCBI
CHM1_19138,561,863 - 138,566,965 (+)NCBI
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001252619   ⟹   NP_001239548
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,521,440 - 135,526,540 (+)NCBI
GRCh379138,413,284 - 138,418,386 (+)NCBI
HuRef9107,875,074 - 107,880,176 (+)NCBI
CHM1_19138,561,863 - 138,566,965 (+)NCBI
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBI
Sequence:
RefSeq Acc Id: NM_002297   ⟹   NP_002288
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,521,440 - 135,526,540 (+)NCBI
GRCh379138,413,284 - 138,418,386 (+)NCBI
Build 369137,553,107 - 137,558,199 (+)NCBI Archive
HuRef9107,875,074 - 107,880,176 (+)NCBI
CHM1_19138,561,863 - 138,566,965 (+)NCBI
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011518675   ⟹   XP_011516977
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,521,440 - 135,525,158 (+)NCBI
Sequence:
RefSeq Acc Id: XM_047423375   ⟹   XP_047279331
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,523,932 - 135,526,540 (+)NCBI
RefSeq Acc Id: XM_054362961   ⟹   XP_054218936
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.09147,749,482 - 147,753,200 (+)NCBI
RefSeq Acc Id: XM_054362962   ⟹   XP_054218937
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.09147,752,545 - 147,754,582 (+)NCBI
RefSeq Acc Id: NP_002288   ⟸   NM_002297
- Peptide Label: isoform 1 precursor
- UniProtKB: Q5VSP4 (UniProtKB/Swiss-Prot),   Q5T8A1 (UniProtKB/Swiss-Prot),   P31025 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001239546   ⟸   NM_001252617
- Peptide Label: isoform 1 precursor
- UniProtKB: Q5VSP4 (UniProtKB/Swiss-Prot),   Q5T8A1 (UniProtKB/Swiss-Prot),   P31025 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001239547   ⟸   NM_001252618
- Peptide Label: isoform 2 precursor
- UniProtKB: P31025 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001239548   ⟸   NM_001252619
- Peptide Label: isoform 3 precursor
- UniProtKB: P31025 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011516977   ⟸   XM_011518675
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSP00000360846   ⟸   ENST00000371781
Ensembl Acc Id: ENSP00000263598   ⟸   ENST00000263598
RefSeq Acc Id: XP_047279331   ⟸   XM_047423375
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054218936   ⟸   XM_054362961
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054218937   ⟸   XM_054362962
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P31025-F1-model_v2 AlphaFold P31025 1-176 view protein structure

Promoters
RGD ID:7216603
Promoter ID:EPDNEW_H14047
Type:single initiation site
Name:LCN1_1
Description:lipocalin 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
GRCh389135,521,440 - 135,521,500EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:6525 AgrOrtholog
COSMIC LCN1 COSMIC
Ensembl Genes ENSG00000160349 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000263598 ENTREZGENE
  ENST00000263598.6 UniProtKB/Swiss-Prot
  ENST00000371781 ENTREZGENE
  ENST00000371781.4 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot
GTEx ENSG00000160349 GTEx
HGNC ID HGNC:6525 ENTREZGENE
Human Proteome Map LCN1 Human Proteome Map
InterPro Calycin UniProtKB/Swiss-Prot
  Lipocalin UniProtKB/Swiss-Prot
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot
  von_Ebner_gland UniProtKB/Swiss-Prot
KEGG Report hsa:3933 UniProtKB/Swiss-Prot
NCBI Gene 3933 ENTREZGENE
OMIM 151675 OMIM
PANTHER LIPOCALIN-1 UniProtKB/Swiss-Prot
  PTHR11430 UniProtKB/Swiss-Prot
Pfam Lipocalin UniProtKB/Swiss-Prot
PharmGKB PA30308 PharmGKB
PRINTS VNEBNERGLAND UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot
UniProt LCN1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q5T8A1 ENTREZGENE
  Q5VSP4 ENTREZGENE
UniProt Secondary Q5T8A1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-11-22 LCN1  lipocalin 1  LCN1  lipocalin 1 (tear prealbumin)  Symbol and/or name change 5135510 APPROVED