LRIF1 (ligand dependent nuclear receptor interacting factor 1) - Rat Genome Database

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Gene: LRIF1 (ligand dependent nuclear receptor interacting factor 1) Homo sapiens
Analyze
Symbol: LRIF1
Name: ligand dependent nuclear receptor interacting factor 1
RGD ID: 1603986
HGNC Page HGNC:30299
Description: Predicted to enable nuclear retinoic acid receptor binding activity. Involved in dosage compensation by inactivation of X chromosome. Located in centriolar satellite; chromosome, telomeric region; and nuclear lumen. Implicated in facioscapulohumeral muscular dystrophy 3.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C1orf103; FLJ11269; FSHD3; HBiX1; HP1-binding protein enriched in inactive X chromosome protein 1; ligand-dependent nuclear receptor-interacting factor 1; receptor interacting factor 1; receptor-interacting factor 1; RIF1; RP11-96K19.1
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
GRCh381110,874,957 - 110,963,922 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1110,947,190 - 110,963,965 (-)EnsemblGRCh38hg38GRCh38
GRCh371111,489,812 - 111,506,544 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361111,291,335 - 111,308,089 (-)NCBINCBI36Build 36hg18NCBI36
Celera1109,736,827 - 109,753,586 (-)NCBICelera
Cytogenetic Map1p13.3NCBI
HuRef1109,361,082 - 109,377,847 (-)NCBIHuRef
CHM1_11111,604,955 - 111,621,714 (-)NCBICHM1_1
T2T-CHM13v2.01110,888,014 - 110,978,737 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:15383276   PMID:15489334   PMID:16169070   PMID:16189514   PMID:16710414   PMID:17207965   PMID:17455211   PMID:18029348   PMID:18187620   PMID:20562864  
PMID:20850016   PMID:21873635   PMID:21888893   PMID:21900206   PMID:23251661   PMID:23542155   PMID:24270157   PMID:24981860   PMID:25281560   PMID:26186194   PMID:26496610   PMID:26638075  
PMID:27705803   PMID:28514442   PMID:29478914   PMID:30016453   PMID:30194290   PMID:30415952   PMID:30463901   PMID:30804394   PMID:30804502   PMID:31091453   PMID:31180492   PMID:32296183  
PMID:32707033   PMID:32814053   PMID:33961781   PMID:34079125   PMID:34189442   PMID:34780483   PMID:35140242   PMID:35271311   PMID:35439318   PMID:35944360   PMID:36089195   PMID:36543142  
PMID:36966392   PMID:37059091   PMID:37071664   PMID:37380887   PMID:37827155   PMID:38297188   PMID:38580884  


Genomics

Comparative Map Data
LRIF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381110,874,957 - 110,963,922 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1110,947,190 - 110,963,965 (-)EnsemblGRCh38hg38GRCh38
GRCh371111,489,812 - 111,506,544 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361111,291,335 - 111,308,089 (-)NCBINCBI36Build 36hg18NCBI36
Celera1109,736,827 - 109,753,586 (-)NCBICelera
Cytogenetic Map1p13.3NCBI
HuRef1109,361,082 - 109,377,847 (-)NCBIHuRef
CHM1_11111,604,955 - 111,621,714 (-)NCBICHM1_1
T2T-CHM13v2.01110,888,014 - 110,978,737 (-)NCBIT2T-CHM13v2.0
Lrif1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393106,592,256 - 106,643,893 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3106,592,303 - 106,643,893 (+)EnsemblGRCm39 Ensembl
GRCm383106,684,942 - 106,736,577 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3106,684,987 - 106,736,577 (+)EnsemblGRCm38mm10GRCm38
MGSCv373106,487,905 - 106,539,495 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363106,813,043 - 106,864,633 (+)NCBIMGSCv36mm8
Celera3109,014,195 - 109,065,756 (+)NCBICelera
Cytogenetic Map3F2.3NCBI
cM Map346.52NCBI
Lrif1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82196,919,606 - 197,010,713 (+)NCBIGRCr8
mRatBN7.22194,231,397 - 194,322,489 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2194,230,951 - 194,322,483 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2201,940,483 - 201,955,702 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02199,821,012 - 199,836,011 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02194,637,976 - 194,652,979 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02209,358,668 - 209,448,123 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2209,358,760 - 209,448,123 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02228,824,841 - 228,915,197 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42202,141,413 - 202,156,437 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12202,114,300 - 202,118,423 (+)NCBI
Celera2186,977,203 - 186,992,223 (+)NCBICelera
Cytogenetic Map2q34NCBI
Lrif1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543514,469,488 - 14,484,632 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543514,467,123 - 14,485,109 (-)NCBIChiLan1.0ChiLan1.0
LRIF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21116,074,468 - 116,165,837 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11115,222,961 - 115,244,582 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01113,523,567 - 113,611,043 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11126,736,014 - 126,822,457 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1126,736,039 - 126,752,907 (+)Ensemblpanpan1.1panPan2
LRIF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1641,023,383 - 41,041,776 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl641,023,787 - 41,039,844 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha643,800,911 - 43,817,578 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0641,355,242 - 41,371,890 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl641,355,239 - 41,373,594 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1641,075,870 - 41,092,367 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0641,046,009 - 41,062,678 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0641,481,388 - 41,498,059 (+)NCBIUU_Cfam_GSD_1.0
Lrif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505817,780,265 - 17,800,223 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367042,319,145 - 2,333,400 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367042,313,923 - 2,334,839 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRIF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4109,271,728 - 109,292,310 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14109,271,562 - 109,292,313 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24119,639,087 - 119,657,813 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRIF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12022,598,160 - 22,614,752 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2022,598,124 - 22,617,024 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603835,852,586 - 35,869,524 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrif1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247726,713,055 - 6,733,608 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247726,713,224 - 6,733,841 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LRIF1
70 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p13.3-12(chr1:109756630-118650204)x3 copy number gain See cases [RCV000051827] Chr1:109756630..118650204 [GRCh38]
Chr1:110299252..119192827 [GRCh37]
Chr1:110100775..118994350 [NCBI36]
Chr1:1p13.3-12		 pathogenic
GRCh38/hg38 1p21.2-13.2(chr1:101618097-111703028)x1 copy number loss See cases [RCV000053879] Chr1:101618097..111703028 [GRCh38]
Chr1:102083653..112245650 [GRCh37]
Chr1:101856241..112047173 [NCBI36]
Chr1:1p21.2-13.2		 pathogenic
NM_001006945.1(LRIF1):c.183C>T (p.Phe61=) single nucleotide variant Malignant melanoma [RCV000059833] Chr1:110949929 [GRCh38]
Chr1:111492551 [GRCh37]
Chr1:111294074 [NCBI36]
Chr1:1p13.3		 not provided
NM_001006945.1(LRIF1):c.-12-616G>A single nucleotide variant Lung cancer [RCV000089716] Chr1:110950739 [GRCh38]
Chr1:111493361 [GRCh37]
Chr1:1p13.3		 uncertain significance
GRCh38/hg38 1p21.1-12(chr1:104325484-119977655)x3 copy number gain See cases [RCV000142953] Chr1:104325484..119977655 [GRCh38]
Chr1:104868106..120471049 [GRCh37]
Chr1:104669629..120321801 [NCBI36]
Chr1:1p21.1-12		 pathogenic
GRCh38/hg38 1p21.1-13.2(chr1:105468292-112190626)x1 copy number loss See cases [RCV000142760] Chr1:105468292..112190626 [GRCh38]
Chr1:106010914..112733248 [GRCh37]
Chr1:105812437..112534771 [NCBI36]
Chr1:1p21.1-13.2		 pathogenic
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12		 likely benign
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3 copy number gain See cases [RCV000512354] Chr1:93837992..121343783 [GRCh37]
Chr1:1p22.1-11.2		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NC_000001.11:g.(?_103175204)_(111410059_?)del deletion Autism [RCV000754122] Chr1:103175204..111410059 [GRCh38]
Chr1:1p21.1-13.2		 likely pathogenic
GRCh37/hg19 1p22.1-13.3(chr1:94054724-111671707)x3 copy number gain not provided [RCV000749068] Chr1:94054724..111671707 [GRCh37]
Chr1:1p22.1-13.3		 pathogenic
NM_018372.4(LRIF1):c.869_872dup (p.Trp291Ter) duplication Facioscapulohumeral muscular dystrophy 3, digenic [RCV001568343] Chr1:110952011..110952012 [GRCh38]
Chr1:111494633..111494634 [GRCh37]
Chr1:1p13.3		 pathogenic
GRCh37/hg19 1p13.3-13.2(chr1:110994179-112360446)x1 copy number loss not provided [RCV000849607] Chr1:110994179..112360446 [GRCh37]
Chr1:1p13.3-13.2		 pathogenic
NC_000001.10:g.(?_108679275)_(111674176_?)del deletion Hereditary spastic paraplegia 63 [RCV003105726] Chr1:108679275..111674176 [GRCh37]
Chr1:1p13.3		 pathogenic
GRCh37/hg19 1p21.2-12(chr1:102021465-119737478) copy number loss Seizure [RCV001352640] Chr1:102021465..119737478 [GRCh37]
Chr1:1p21.2-12		 pathogenic
NC_000001.10:g.(?_111506243)_(111745058_?)dup duplication not provided [RCV001309951] Chr1:111506243..111745058 [GRCh37]
Chr1:1p13.3		 uncertain significance
GRCh37/hg19 1p21.3-13.2(chr1:95046805-114714931) copy number loss not specified [RCV002053503] Chr1:95046805..114714931 [GRCh37]
Chr1:1p21.3-13.2		 pathogenic
NC_000001.10:g.(?_111145905)_(114454813_?)del deletion not provided [RCV003113195] Chr1:111145905..114454813 [GRCh37]
Chr1:1p13.3-13.2		 pathogenic
NM_018372.4(LRIF1):c.2201C>T (p.Pro734Leu) single nucleotide variant not specified [RCV004191978] Chr1:110948068 [GRCh38]
Chr1:111490690 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.2275C>A (p.Leu759Ile) single nucleotide variant not specified [RCV004139123] Chr1:110947994 [GRCh38]
Chr1:111490616 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.569T>C (p.Ile190Thr) single nucleotide variant not specified [RCV004152086] Chr1:110897873 [GRCh38]
Chr1:111440495 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1364C>A (p.Thr455Lys) single nucleotide variant not specified [RCV004217009] Chr1:110951520 [GRCh38]
Chr1:111494142 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1219A>C (p.Ile407Leu) single nucleotide variant not specified [RCV004212756] Chr1:110951665 [GRCh38]
Chr1:111494287 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1919A>G (p.His640Arg) single nucleotide variant not specified [RCV004158248] Chr1:110948350 [GRCh38]
Chr1:111490972 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.317A>T (p.Tyr106Phe) single nucleotide variant not specified [RCV004214184] Chr1:110952567 [GRCh38]
Chr1:111495189 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.266C>G (p.Thr89Arg) single nucleotide variant not specified [RCV004144317] Chr1:110952618 [GRCh38]
Chr1:111495240 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.632C>A (p.Ala211Glu) single nucleotide variant not specified [RCV004175761] Chr1:110952252 [GRCh38]
Chr1:111494874 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1429A>G (p.Ile477Val) single nucleotide variant not specified [RCV004157455] Chr1:110951455 [GRCh38]
Chr1:111494077 [GRCh37]
Chr1:1p13.3		 likely benign
NM_018372.4(LRIF1):c.2246A>G (p.Lys749Arg) single nucleotide variant not specified [RCV004204507] Chr1:110948023 [GRCh38]
Chr1:111490645 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.316T>G (p.Tyr106Asp) single nucleotide variant not specified [RCV004214182] Chr1:110952568 [GRCh38]
Chr1:111495190 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.371G>A (p.Arg124His) single nucleotide variant not specified [RCV004141380] Chr1:110895003 [GRCh38]
Chr1:111437625 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1360A>G (p.Thr454Ala) single nucleotide variant not specified [RCV004175435] Chr1:110951524 [GRCh38]
Chr1:111494146 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.424C>G (p.Leu142Val) single nucleotide variant not specified [RCV004098963] Chr1:110896653 [GRCh38]
Chr1:111439275 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1547C>A (p.Ala516Glu) single nucleotide variant not specified [RCV004134752] Chr1:110951337 [GRCh38]
Chr1:111493959 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.190A>C (p.Met64Leu) single nucleotide variant not specified [RCV004086075] Chr1:110952694 [GRCh38]
Chr1:111495316 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.2014A>G (p.Thr672Ala) single nucleotide variant not specified [RCV004315492] Chr1:110948255 [GRCh38]
Chr1:111490877 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.2262G>C (p.Glu754Asp) single nucleotide variant not specified [RCV004274526] Chr1:110948007 [GRCh38]
Chr1:111490629 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.478T>C (p.Ser160Pro) single nucleotide variant not specified [RCV004263443] Chr1:110896707 [GRCh38]
Chr1:111439329 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.211A>G (p.Asn71Asp) single nucleotide variant not specified [RCV004285031] Chr1:110952673 [GRCh38]
Chr1:111495295 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.784A>G (p.Ile262Val) single nucleotide variant not specified [RCV004276523] Chr1:110952100 [GRCh38]
Chr1:111494722 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.419T>C (p.Val140Ala) single nucleotide variant not specified [RCV004249594] Chr1:110952465 [GRCh38]
Chr1:111495087 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1976A>T (p.Asn659Ile) single nucleotide variant not specified [RCV004266325] Chr1:110948293 [GRCh38]
Chr1:111490915 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.2176G>A (p.Glu726Lys) single nucleotide variant not specified [RCV004259191] Chr1:110948093 [GRCh38]
Chr1:111490715 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1601A>G (p.His534Arg) single nucleotide variant not specified [RCV004255700] Chr1:110950119 [GRCh38]
Chr1:111492741 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.134A>G (p.His45Arg) single nucleotide variant not specified [RCV004360438] Chr1:110892415 [GRCh38]
Chr1:111435037 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1222T>G (p.Ser408Ala) single nucleotide variant not specified [RCV004363890] Chr1:110951662 [GRCh38]
Chr1:111494284 [GRCh37]
Chr1:1p13.3		 uncertain significance
GRCh37/hg19 1p13.3-13.1(chr1:110066946-116672408)x1 copy number loss not provided [RCV003483294] Chr1:110066946..116672408 [GRCh37]
Chr1:1p13.3-13.1		 pathogenic
GRCh37/hg19 1p13.3-13.2(chr1:109483388-112293512)x1 copy number loss not provided [RCV003483272] Chr1:109483388..112293512 [GRCh37]
Chr1:1p13.3-13.2		 pathogenic
GRCh37/hg19 1p13.3(chr1:111346683-111679264)x1 copy number loss not provided [RCV003483305] Chr1:111346683..111679264 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1035G>A (p.Thr345=) single nucleotide variant not provided [RCV003406668] Chr1:110951849 [GRCh38]
Chr1:111494471 [GRCh37]
Chr1:1p13.3		 likely benign
GRCh37/hg19 1p13.3-13.2(chr1:111277065-111804157)x1 copy number loss not specified [RCV003986462] Chr1:111277065..111804157 [GRCh37]
Chr1:1p13.3-13.2		 uncertain significance
GRCh37/hg19 1p13.3-13.2(chr1:109700156-112176616)x1 copy number loss not specified [RCV003987183] Chr1:109700156..112176616 [GRCh37]
Chr1:1p13.3-13.2		 uncertain significance
NM_000560.4(CD53):c.553A>G (p.Ile185Val) single nucleotide variant not specified [RCV004435489] Chr1:110897857 [GRCh38]
Chr1:111440479 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.163G>A (p.Val55Met) single nucleotide variant not specified [RCV004435488] Chr1:110892444 [GRCh38]
Chr1:111435066 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1129T>C (p.Ser377Pro) single nucleotide variant not specified [RCV004410820] Chr1:110951755 [GRCh38]
Chr1:111494377 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1207C>A (p.Pro403Thr) single nucleotide variant not specified [RCV004410821] Chr1:110951677 [GRCh38]
Chr1:111494299 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1414T>G (p.Leu472Val) single nucleotide variant not specified [RCV004410822] Chr1:110951470 [GRCh38]
Chr1:111494092 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1483G>A (p.Val495Ile) single nucleotide variant not specified [RCV004410823] Chr1:110951401 [GRCh38]
Chr1:111494023 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.148A>C (p.Lys50Gln) single nucleotide variant not specified [RCV004410824] Chr1:110952736 [GRCh38]
Chr1:111495358 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1547C>G (p.Ala516Gly) single nucleotide variant not specified [RCV004410825] Chr1:110951337 [GRCh38]
Chr1:111493959 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.53G>A (p.Gly18Asp) single nucleotide variant not specified [RCV004410828] Chr1:110963636 [GRCh38]
Chr1:111506258 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.2174C>T (p.Thr725Ile) single nucleotide variant not specified [RCV004410827] Chr1:110948095 [GRCh38]
Chr1:111490717 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1957A>G (p.Ile653Val) single nucleotide variant not specified [RCV004410826] Chr1:110948312 [GRCh38]
Chr1:111490934 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.724G>A (p.Val242Ile) single nucleotide variant not specified [RCV004412899] Chr1:110952160 [GRCh38]
Chr1:111494782 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.761T>C (p.Val254Ala) single nucleotide variant not specified [RCV004412900] Chr1:110952123 [GRCh38]
Chr1:111494745 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1435C>A (p.Pro479Thr) single nucleotide variant not specified [RCV004634104] Chr1:110951449 [GRCh38]
Chr1:111494071 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.643A>T (p.Thr215Ser) single nucleotide variant not specified [RCV004634105] Chr1:110952241 [GRCh38]
Chr1:111494863 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1832A>G (p.Glu611Gly) single nucleotide variant not specified [RCV004637525] Chr1:110949888 [GRCh38]
Chr1:111492510 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1677T>G (p.Asn559Lys) single nucleotide variant not specified [RCV004637524] Chr1:110950043 [GRCh38]
Chr1:111492665 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.821C>T (p.Thr274Ile) single nucleotide variant not specified [RCV004634106] Chr1:110952063 [GRCh38]
Chr1:111494685 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.2288G>A (p.Arg763His) single nucleotide variant not specified [RCV004637519] Chr1:110947981 [GRCh38]
Chr1:111490603 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.58G>T (p.Ala20Ser) single nucleotide variant not specified [RCV004637518] Chr1:110963631 [GRCh38]
Chr1:111506253 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.739C>A (p.Gln247Lys) single nucleotide variant not specified [RCV004637520] Chr1:110952145 [GRCh38]
Chr1:111494767 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.101C>G (p.Thr34Arg) single nucleotide variant not specified [RCV004637522] Chr1:110952783 [GRCh38]
Chr1:111495405 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1908G>T (p.Lys636Asn) single nucleotide variant not specified [RCV004637523] Chr1:110948361 [GRCh38]
Chr1:111490983 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1843A>G (p.Met615Val) single nucleotide variant not specified [RCV004938162] Chr1:110949877 [GRCh38]
Chr1:111492499 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.428A>G (p.Asp143Gly) single nucleotide variant not specified [RCV004938159] Chr1:110952456 [GRCh38]
Chr1:111495078 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1285C>T (p.Leu429Phe) single nucleotide variant not specified [RCV004938163] Chr1:110951599 [GRCh38]
Chr1:111494221 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.934A>G (p.Asn312Asp) single nucleotide variant not specified [RCV004938157] Chr1:110951950 [GRCh38]
Chr1:111494572 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1049T>C (p.Met350Thr) single nucleotide variant not specified [RCV004938158] Chr1:110951835 [GRCh38]
Chr1:111494457 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1094A>G (p.Tyr365Cys) single nucleotide variant not specified [RCV004938160] Chr1:110951790 [GRCh38]
Chr1:111494412 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1387A>G (p.Ser463Gly) single nucleotide variant not specified [RCV004938161] Chr1:110951497 [GRCh38]
Chr1:111494119 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.656G>T (p.Gly219Val) single nucleotide variant not specified [RCV004935125] Chr1:110952228 [GRCh38]
Chr1:111494850 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_018372.4(LRIF1):c.1538C>T (p.Ser513Phe) single nucleotide variant not specified [RCV004935126] Chr1:110951346 [GRCh38]
Chr1:111493968 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.96C>G (p.Ile32Met) single nucleotide variant not specified [RCV004899055] Chr1:110892377 [GRCh38]
Chr1:111434999 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.293C>A (p.Thr98Asn) single nucleotide variant not specified [RCV004899052] Chr1:110894367 [GRCh38]
Chr1:111436989 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_000560.4(CD53):c.449C>T (p.Thr150Met) single nucleotide variant not specified [RCV004899053] Chr1:110896678 [GRCh38]
Chr1:111439300 [GRCh37]
Chr1:1p13.3		 uncertain significance
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1006
Count of miRNA genes:299
Interacting mature miRNAs:341
Transcripts:ENST00000369763, ENST00000485275, ENST00000494675
Prediction methods:Microtar, 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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
597043266GWAS1139340_Hbone mineral content measurement QTL GWAS1139340 (human)0.0000002bone mineral content measurement1110921002110921003Human
1300021BP45_HBlood pressure QTL 45 (human)1.770.00218Blood pressuresystolic1103389009129389009Human
406946347GWAS595323_Hresponse to virus QTL GWAS595323 (human)0.000005response to virus1110875293110875294Human

Markers in Region
RH98723  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371111,506,266 - 111,506,414UniSTSGRCh37
Build 361111,307,789 - 111,307,937RGDNCBI36
Celera1109,753,286 - 109,753,434RGD
Cytogenetic Map1p13.3UniSTS
HuRef1109,377,547 - 109,377,695UniSTS
GeneMap99-GB4 RH Map1356.47UniSTS
AFMb017zg1  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371111,504,484 - 111,504,774UniSTSGRCh37
Build 361111,306,007 - 111,306,297RGDNCBI36
Celera1109,751,504 - 109,751,794RGD
Cytogenetic Map1p13.3UniSTS
HuRef1109,375,761 - 109,376,055UniSTS
Whitehead-RH Map1389.4UniSTS
Whitehead-YAC Contig Map1 UniSTS
EST4F4  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371111,490,580 - 111,490,686UniSTSGRCh37
Build 361111,292,103 - 111,292,209RGDNCBI36
Celera1109,737,595 - 109,737,701RGD
HuRef1109,361,851 - 109,361,957UniSTS


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
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2429 2788 2252 4972 1726 2350 6 624 1950 465 2270 7302 6472 53 3732 1 851 1741 1616 175 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001006945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_018372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005271029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011541768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK001826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK002131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL354713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL360270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL391064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL834466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY190122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC008115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ787643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BU192014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BU664417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD686306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000369763   ⟹   ENSP00000358778
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1110,947,190 - 110,963,922 (-)Ensembl
Ensembl Acc Id: ENST00000485275   ⟹   ENSP00000432290
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1110,947,222 - 110,963,965 (-)Ensembl
Ensembl Acc Id: ENST00000494675   ⟹   ENSP00000435259
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1110,947,191 - 110,952,961 (-)Ensembl
RefSeq Acc Id: NM_001006945   ⟹   NP_001006946
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381110,947,190 - 110,963,922 (-)NCBI
GRCh371111,489,812 - 111,506,825 (-)NCBI
Build 361111,291,335 - 111,308,089 (-)NCBI Archive
Celera1109,736,827 - 109,753,586 (-)RGD
HuRef1109,361,082 - 109,377,847 (-)RGD
CHM1_11111,604,955 - 111,621,714 (-)NCBI
T2T-CHM13v2.01110,961,987 - 110,978,737 (-)NCBI
Sequence:
RefSeq Acc Id: NM_018372   ⟹   NP_060842
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381110,947,190 - 110,963,922 (-)NCBI
GRCh371111,489,812 - 111,506,825 (-)NCBI
Build 361111,291,335 - 111,308,089 (-)NCBI Archive
Celera1109,736,827 - 109,753,586 (-)RGD
HuRef1109,361,082 - 109,377,847 (-)RGD
CHM1_11111,604,955 - 111,621,714 (-)NCBI
T2T-CHM13v2.01110,961,987 - 110,978,737 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005271029   ⟹   XP_005271086
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381110,947,190 - 110,963,922 (-)NCBI
GRCh371111,489,812 - 111,506,825 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017001769   ⟹   XP_016857258
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381110,874,957 - 110,963,922 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054337631   ⟹   XP_054193606
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01110,961,987 - 110,978,737 (-)NCBI
RefSeq Acc Id: XM_054337632   ⟹   XP_054193607
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01110,888,014 - 110,978,737 (-)NCBI
RefSeq Acc Id: NP_060842   ⟸   NM_018372
- Peptide Label: isoform 1
- UniProtKB: Q9NUM5 (UniProtKB/Swiss-Prot),   Q96HT4 (UniProtKB/Swiss-Prot),   Q8N3B6 (UniProtKB/Swiss-Prot),   Q86XS4 (UniProtKB/Swiss-Prot),   Q9NV32 (UniProtKB/Swiss-Prot),   Q5T3J3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001006946   ⟸   NM_001006945
- Peptide Label: isoform 2
- UniProtKB: Q5T3J3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_005271086   ⟸   XM_005271029
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016857258   ⟸   XM_017001769
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSP00000435259   ⟸   ENST00000494675
Ensembl Acc Id: ENSP00000432290   ⟸   ENST00000485275
Ensembl Acc Id: ENSP00000358778   ⟸   ENST00000369763
RefSeq Acc Id: XP_054193607   ⟸   XM_054337632
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054193606   ⟸   XM_054337631
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5T3J3-F1-model_v2 AlphaFold Q5T3J3 1-769 view protein structure

Promoters
RGD ID:6784725
Promoter ID:HG_KWN:4084
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_018372,   OTTHUMT00000032934,   UC001EAC.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361111,307,849 - 111,308,349 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:30299 AgrOrtholog
COSMIC LRIF1 COSMIC
Ensembl Genes ENSG00000121931 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000369763 ENTREZGENE
  ENST00000369763.5 UniProtKB/Swiss-Prot
  ENST00000485275 ENTREZGENE
  ENST00000485275.2 UniProtKB/Swiss-Prot
  ENST00000494675.5 UniProtKB/Swiss-Prot
GTEx ENSG00000121931 GTEx
HGNC ID HGNC:30299 ENTREZGENE
Human Proteome Map LRIF1 Human Proteome Map
InterPro LRIF1 UniProtKB/Swiss-Prot
KEGG Report hsa:55791 UniProtKB/Swiss-Prot
NCBI Gene 55791 ENTREZGENE
OMIM 615354 OMIM
PANTHER LIGAND-DEPENDENT NUCLEAR RECEPTOR-INTERACTING FACTOR 1 UniProtKB/Swiss-Prot
  PTHR16131 UniProtKB/Swiss-Prot
Pfam LRIF1 UniProtKB/Swiss-Prot
PharmGKB PA142672487 PharmGKB
UniProt LRIF1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q86XS4 ENTREZGENE
  Q8N3B6 ENTREZGENE
  Q96HT4 ENTREZGENE
  Q9NUM5 ENTREZGENE
  Q9NV32 ENTREZGENE
UniProt Secondary Q86XS4 UniProtKB/Swiss-Prot
  Q8N3B6 UniProtKB/Swiss-Prot
  Q96HT4 UniProtKB/Swiss-Prot
  Q9NUM5 UniProtKB/Swiss-Prot
  Q9NV32 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-27 LRIF1  ligand dependent nuclear receptor interacting factor 1  C1orf103  chromosome 1 open reading frame 103  Symbol and/or name change 5135510 APPROVED