LHFPL4 (LHFPL tetraspan subfamily member 4) - Rat Genome Database

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Gene: LHFPL4 (LHFPL tetraspan subfamily member 4) Homo sapiens
Analyze
Symbol: LHFPL4
Name: LHFPL tetraspan subfamily member 4
RGD ID: 1604456
HGNC Page HGNC:29568
Description: Predicted to enable GABA receptor binding activity. Predicted to be involved in gamma-aminobutyric acid receptor clustering; regulation of inhibitory synapse assembly; and sensory perception of sound. Predicted to be located in dendrite and synapse. Predicted to be active in several cellular components, including GABA-ergic synapse; inhibitory synapse; and postsynaptic membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: GABAA receptor regulatory Lhfpl4; GARLH4; LHFP-like protein 4; lipoma HMGIC fusion partner-like 4; lipoma HMGIC fusion partner-like 4 protein; MGC133162; RP11-58B17.2
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
GRCh3839,498,361 - 9,553,822 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl39,498,361 - 9,553,822 (-)EnsemblGRCh38hg38GRCh38
GRCh3739,540,045 - 9,595,506 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3639,515,045 - 9,570,486 (-)NCBINCBI36Build 36hg18NCBI36
Celera39,474,743 - 9,530,187 (-)NCBICelera
Cytogenetic Map3p25.3NCBI
HuRef39,476,796 - 9,532,110 (-)NCBIHuRef
CHM1_139,490,268 - 9,545,714 (-)NCBICHM1_1
T2T-CHM13v2.039,490,279 - 9,545,747 (-)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

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
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:15905332   PMID:20379614   PMID:21873635   PMID:28279354   PMID:28514442   PMID:28978485   PMID:32296183   PMID:33961781   PMID:36724073   PMID:37433992  


Genomics

Comparative Map Data
LHFPL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3839,498,361 - 9,553,822 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl39,498,361 - 9,553,822 (-)EnsemblGRCh38hg38GRCh38
GRCh3739,540,045 - 9,595,506 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3639,515,045 - 9,570,486 (-)NCBINCBI36Build 36hg18NCBI36
Celera39,474,743 - 9,530,187 (-)NCBICelera
Cytogenetic Map3p25.3NCBI
HuRef39,476,796 - 9,532,110 (-)NCBIHuRef
CHM1_139,490,268 - 9,545,714 (-)NCBICHM1_1
T2T-CHM13v2.039,490,279 - 9,545,747 (-)NCBIT2T-CHM13v2.0
Lhfpl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396113,145,048 - 113,172,345 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6113,145,051 - 113,172,345 (-)EnsemblGRCm39 Ensembl
GRCm386113,168,087 - 113,195,384 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6113,168,090 - 113,195,384 (-)EnsemblGRCm38mm10GRCm38
MGSCv376113,118,081 - 113,145,378 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366113,135,401 - 113,161,161 (-)NCBIMGSCv36mm8
Celera6114,996,909 - 115,024,142 (-)NCBICelera
Cytogenetic Map6E3NCBI
cM Map652.74NCBI
Lhfpl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84147,872,877 - 147,895,770 (-)NCBIGRCr8
mRatBN7.24146,317,110 - 146,340,073 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4146,313,541 - 146,340,463 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4151,701,577 - 151,724,428 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04147,482,411 - 147,505,262 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04146,103,757 - 146,126,678 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04145,117,533 - 145,147,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4145,117,533 - 145,147,397 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04208,415,890 - 208,445,642 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44149,049,668 - 149,072,608 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14149,294,508 - 149,317,449 (-)NCBI
Celera4134,877,048 - 134,898,925 (-)NCBICelera
Cytogenetic Map4q42NCBI
Lhfpl4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555611,066,799 - 1,142,099 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555611,066,799 - 1,142,099 (-)NCBIChiLan1.0ChiLan1.0
LHFPL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v229,510,331 - 9,565,838 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan139,515,093 - 9,570,591 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v039,453,628 - 9,506,434 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.139,695,091 - 9,745,722 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl39,695,091 - 9,745,722 (-)Ensemblpanpan1.1panPan2
LHFPL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1208,630,981 - 8,663,918 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl208,630,747 - 8,660,389 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha208,664,027 - 8,696,484 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0208,660,390 - 8,693,304 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl208,659,943 - 8,693,283 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1208,382,860 - 8,415,261 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0208,727,665 - 8,760,738 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0208,701,291 - 8,734,265 (+)NCBIUU_Cfam_GSD_1.0
Lhfpl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494215,345,648 - 15,396,180 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366023,532,005 - 3,564,680 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366023,532,979 - 3,564,062 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHFPL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1365,869,652 - 65,919,781 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11365,867,124 - 65,920,887 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21372,937,834 - 72,987,503 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LHFPL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12245,502,763 - 45,556,828 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041121,008,266 - 121,060,209 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhfpl4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247314,194,321 - 4,222,105 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247314,194,321 - 4,222,400 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LHFPL4
10 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p25.3(chr3:9221810-9727021)x3 copy number gain See cases [RCV000050855] Chr3:9221810..9727021 [GRCh38]
Chr3:9263494..9768705 [GRCh37]
Chr3:9238494..9743705 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.3(chr3:52266-11089569)x1 copy number loss See cases [RCV000051447] Chr3:52266..11089569 [GRCh38]
Chr3:93949..11131255 [GRCh37]
Chr3:68949..11106255 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-9507969)x1 copy number loss See cases [RCV000051476] Chr3:63843..9507969 [GRCh38]
Chr3:105526..9549653 [GRCh37]
Chr3:80526..9524653 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p25.3-25.2(chr3:8581778-12015238)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051480]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051480]|See cases [RCV000051480] Chr3:8581778..12015238 [GRCh38]
Chr3:8623464..12056738 [GRCh37]
Chr3:8598464..12031738 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
GRCh38/hg38 3p25.3(chr3:9393349-9956171)x1 copy number loss See cases [RCV000051481] Chr3:9393349..9956171 [GRCh38]
Chr3:9435033..9997855 [GRCh37]
Chr3:9410033..9972855 [NCBI36]
Chr3:3p25.3		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
NM_198560.2(LHFPL4):c.737G>A (p.Gly246Glu) single nucleotide variant Malignant melanoma [RCV000060876] Chr3:9502218 [GRCh38]
Chr3:9543902 [GRCh37]
Chr3:9518902 [NCBI36]
Chr3:3p25.3		 not provided
GRCh38/hg38 3p26.1-25.3(chr3:8038727-11240931)x4 copy number gain See cases [RCV000135641] Chr3:8038727..11240931 [GRCh38]
Chr3:8080414..11282617 [GRCh37]
Chr3:8055414..11257617 [NCBI36]
Chr3:3p26.1-25.3		 likely pathogenic
GRCh38/hg38 3p25.3-25.2(chr3:9394874-11690612)x1 copy number loss See cases [RCV000137433] Chr3:9394874..11690612 [GRCh38]
Chr3:9436558..11732086 [GRCh37]
Chr3:9411558..11707086 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
GRCh38/hg38 3p26.1-25.2(chr3:7975734-12636917)x3 copy number gain See cases [RCV000137309] Chr3:7975734..12636917 [GRCh38]
Chr3:8017421..12678416 [GRCh37]
Chr3:7992421..12653416 [NCBI36]
Chr3:3p26.1-25.2		 likely pathogenic
GRCh38/hg38 3p25.3(chr3:8812036-9953438)x3 copy number gain See cases [RCV000137329] Chr3:8812036..9953438 [GRCh38]
Chr3:8853722..9995122 [GRCh37]
Chr3:8828722..9970122 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.2(chr3:32241-12681483)x1 copy number loss See cases [RCV000138143] Chr3:32241..12681483 [GRCh38]
Chr3:73914..12722982 [GRCh37]
Chr3:48914..12697982 [NCBI36]
Chr3:3p26.3-25.2		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-11379835)x1 copy number loss See cases [RCV000138376] Chr3:32241..11379835 [GRCh38]
Chr3:73914..11421309 [GRCh37]
Chr3:48914..11396309 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic|likely benign
GRCh38/hg38 3p25.3(chr3:8941623-10151752)x3 copy number gain See cases [RCV000138535] Chr3:8941623..10151752 [GRCh38]
Chr3:8983307..10193436 [GRCh37]
Chr3:8958307..10168436 [NCBI36]
Chr3:3p25.3		 likely benign|uncertain significance
GRCh38/hg38 3p25.3(chr3:9142303-9793982)x3 copy number gain See cases [RCV000139348] Chr3:9142303..9793982 [GRCh38]
Chr3:9183987..9835666 [GRCh37]
Chr3:9158987..9810666 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9574994)x1 copy number loss See cases [RCV000140239] Chr3:32241..9574994 [GRCh38]
Chr3:73914..9616678 [GRCh37]
Chr3:48914..9591678 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-11221602)x1 copy number loss See cases [RCV000141731] Chr3:20213..11221602 [GRCh38]
Chr3:61891..11263288 [GRCh37]
Chr3:36891..11238288 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10323124)x1 copy number loss See cases [RCV000143325] Chr3:32241..10323124 [GRCh38]
Chr3:73914..10364808 [GRCh37]
Chr3:48914..10339808 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10631310)x1 copy number loss See cases [RCV000143173] Chr3:32241..10631310 [GRCh38]
Chr3:73914..10672995 [GRCh37]
Chr3:48914..10647995 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:688897-11051142)x1 copy number loss See cases [RCV000143706] Chr3:688897..11051142 [GRCh38]
Chr3:730581..11092828 [GRCh37]
Chr3:705581..11067828 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p25.3(chr3:9405337-10168892)x3 copy number gain See cases [RCV000240180] Chr3:9405337..10168892 [GRCh37]
Chr3:3p25.3		 likely pathogenic
GRCh37/hg19 3p25.3-25.2(chr3:8922160-12338637)x1 copy number loss See cases [RCV000240139] Chr3:8922160..12338637 [GRCh37]
Chr3:3p25.3-25.2		 pathogenic
GRCh37/hg19 3p25.3(chr3:9518530-9547865)x3 copy number gain See cases [RCV000240499] Chr3:9518530..9547865 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh37/hg19 3p26.3-24.2(chr3:61891-24432821)x3 copy number gain See cases [RCV000447247] Chr3:61891..24432821 [GRCh37]
Chr3:3p26.3-24.2		 pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181)x3 copy number gain See cases [RCV000448528] Chr3:61891..36710181 [GRCh37]
Chr3:3p26.3-22.2		 pathogenic
GRCh37/hg19 3p26.1-25.3(chr3:6842555-10153209)x1 copy number loss See cases [RCV000448839] Chr3:6842555..10153209 [GRCh37]
Chr3:3p26.1-25.3		 pathogenic
GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3 copy number gain See cases [RCV000510429] Chr3:61891..33958201 [GRCh37]
Chr3:3p26.3-22.3		 pathogenic
GRCh37/hg19 3p25.3(chr3:9421663-9574327)x1 copy number loss See cases [RCV000511930] Chr3:9421663..9574327 [GRCh37]
Chr3:3p25.3		 likely pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-37459464)x3 copy number gain See cases [RCV000511463] Chr3:61891..37459464 [GRCh37]
Chr3:3p26.3-22.2		 pathogenic
GRCh37/hg19 3p26.3-25.2(chr3:61891-12575409)x1 copy number loss See cases [RCV000511155] Chr3:61891..12575409 [GRCh37]
Chr3:3p26.3-25.2		 pathogenic
GRCh37/hg19 3p25.3(chr3:9371390-9599828)x4 copy number gain See cases [RCV000510969] Chr3:9371390..9599828 [GRCh37]
Chr3:3p25.3		 likely benign
NM_198560.3(LHFPL4):c.268A>G (p.Ser90Gly) single nucleotide variant not specified [RCV004310539] Chr3:9552412 [GRCh38]
Chr3:9594096 [GRCh37]
Chr3:3p25.3		 likely benign
NM_198560.3(LHFPL4):c.164A>G (p.Lys55Arg) single nucleotide variant not specified [RCV004307132] Chr3:9552516 [GRCh38]
Chr3:9594200 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-25.3(chr3:61891-10104842)x1 copy number loss not provided [RCV000682180] Chr3:61891..10104842 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p26.3-24.3(chr3:1897972-19519085)x3 copy number gain not provided [RCV000682215] Chr3:1897972..19519085 [GRCh37]
Chr3:3p26.3-24.3		 pathogenic
GRCh37/hg19 3p26.1-24.3(chr3:5173870-16760262)x3 copy number gain not provided [RCV000682233] Chr3:5173870..16760262 [GRCh37]
Chr3:3p26.1-24.3		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p25.3(chr3:9547959-9898582)x1 copy number loss not provided [RCV000742227] Chr3:9547959..9898582 [GRCh37]
Chr3:3p25.3		 benign
GRCh37/hg19 3p25.3(chr3:9561205-9568424)x1 copy number loss not provided [RCV000742228] Chr3:9561205..9568424 [GRCh37]
Chr3:3p25.3		 benign
GRCh37/hg19 3p25.3(chr3:8883205-9954034)x3 copy number gain not provided [RCV000848799] Chr3:8883205..9954034 [GRCh37]
Chr3:3p25.3		 uncertain significance
Single allele duplication Neurodevelopmental disorder [RCV000787461] Chr3:9453917..12015126 [GRCh37]
Chr3:3p25.3-25.2		 uncertain significance
GRCh37/hg19 3p26.1-25.3(chr3:7172720-9545741)x3 copy number gain not provided [RCV001005411] Chr3:7172720..9545741 [GRCh37]
Chr3:3p26.1-25.3		 uncertain significance
GRCh37/hg19 3p26.3-25.3(chr3:61891-10287825)x1 copy number loss not provided [RCV001007530] Chr3:61891..10287825 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
NC_000003.11:g.(?_8775553)_(9730776_?)dup duplication Long QT syndrome [RCV001033330] Chr3:8775553..9730776 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh37/hg19 3p26.3-25.3(chr3:60931-10687964)x3 copy number gain not provided [RCV002468435] Chr3:60931..10687964 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p26.3-25.3(chr3:61892-11679509)x1 copy number loss not provided [RCV002473616] Chr3:61892..11679509 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p26.1-25.3(chr3:7694117-9546173)x1 copy number loss See cases [RCV002285054] Chr3:7694117..9546173 [GRCh37]
Chr3:3p26.1-25.3		 pathogenic
GRCh37/hg19 3p25.3(chr3:9501646-9991928)x4 copy number gain not provided [RCV001795849] Chr3:9501646..9991928 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181) copy number gain not specified [RCV002053300] Chr3:61891..36710181 [GRCh37]
Chr3:3p26.3-22.2		 pathogenic
GRCh37/hg19 3p26.3-24.2(chr3:61891-24432821) copy number gain not specified [RCV002053299] Chr3:61891..24432821 [GRCh37]
Chr3:3p26.3-24.2		 pathogenic
GRCh37/hg19 3p26.3-25.3(chr3:61891-9797094) copy number loss not specified [RCV002053298] Chr3:61891..9797094 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p26.1-25.3(chr3:6842555-10153209) copy number loss not specified [RCV002053327] Chr3:6842555..10153209 [GRCh37]
Chr3:3p26.1-25.3		 pathogenic
NC_000003.11:g.(?_7782024)_(11078652_?)dup duplication Atrioventricular septal defect, susceptibility to, 2 [RCV001875165] Chr3:7782024..11078652 [GRCh37]
Chr3:3p26.1-25.3		 uncertain significance
NC_000003.11:g.(?_8775563)_(9986075_?)dup duplication Long QT syndrome [RCV001923348] Chr3:8775563..9986075 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_198560.3(LHFPL4):c.340T>G (p.Ser114Ala) single nucleotide variant not specified [RCV004310540] Chr3:9552340 [GRCh38]
Chr3:9594024 [GRCh37]
Chr3:3p25.3		 likely benign
GRCh37/hg19 3p26.3-25.3(chr3:61892-9769457)x1 copy number loss not provided [RCV002472587] Chr3:61892..9769457 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p26.3-25.3(chr3:61892-9899605)x1 copy number loss not provided [RCV002472571] Chr3:61892..9899605 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1 copy number loss 3p- syndrome [RCV003330127] Chr3:3691505..9917651 [GRCh37]
Chr3:3p26.2-25.3		 pathogenic
GRCh37/hg19 3p26.3-24.1(chr3:310747-28297447)x3 copy number gain not provided [RCV003484107] Chr3:310747..28297447 [GRCh37]
Chr3:3p26.3-24.1		 pathogenic
Single allele deletion not provided [RCV003448703] Chr3:61435..9944653 [GRCh37]
Chr3:3p26.3-25.3		 pathogenic
NM_198560.3(LHFPL4):c.378G>T (p.Lys126Asn) single nucleotide variant not specified [RCV004414989] Chr3:9552302 [GRCh38]
Chr3:9593986 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_198560.3(LHFPL4):c.289T>C (p.Phe97Leu) single nucleotide variant not specified [RCV004414985] Chr3:9552391 [GRCh38]
Chr3:9594075 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh37/hg19 3p26.1-25.3(chr3:6306331-11468530)x1 copy number loss not specified [RCV003986402] Chr3:6306331..11468530 [GRCh37]
Chr3:3p26.1-25.3		 pathogenic
GRCh37/hg19 3p26.3-22.3(chr3:61891-33946644)x3 copy number gain not specified [RCV003986437] Chr3:61891..33946644 [GRCh37]
Chr3:3p26.3-22.3		 pathogenic
NM_198560.3(LHFPL4):c.418G>A (p.Val140Ile) single nucleotide variant not specified [RCV004414990] Chr3:9506192 [GRCh38]
Chr3:9547876 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_198560.3(LHFPL4):c.628A>C (p.Lys210Gln) single nucleotide variant not specified [RCV004414991] Chr3:9505982 [GRCh38]
Chr3:9547666 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_198560.3(LHFPL4):c.370G>C (p.Val124Leu) single nucleotide variant not specified [RCV004414986] Chr3:9552310 [GRCh38]
Chr3:9593994 [GRCh37]
Chr3:3p25.3		 uncertain significance
GRCh37/hg19 3p26.3-22.3(chr3:60000-34461438)x3 copy number gain not provided [RCV004577500] Chr3:60000..34461438 [GRCh37]
Chr3:3p26.3-22.3		 pathogenic
NC_000003.11:g.(?_9470623)_(11078652_?)dup duplication not provided [RCV004582249] Chr3:9470623..11078652 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_198560.3(LHFPL4):c.335G>T (p.Cys112Phe) single nucleotide variant not specified [RCV004642450] Chr3:9552345 [GRCh38]
Chr3:9594029 [GRCh37]
Chr3:3p25.3		 uncertain significance
NM_198560.3(LHFPL4):c.624G>C (p.Glu208Asp) single nucleotide variant not specified [RCV004642449] Chr3:9505986 [GRCh38]
Chr3:9547670 [GRCh37]
Chr3:3p25.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:886
Count of miRNA genes:562
Interacting mature miRNAs:622
Transcripts:ENST00000287585, ENST00000495730, ENST00000498277
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316345GLUCO224_HGlucose level QTL 224 (human)1.270.008Glucose level3121543441Human
407321401GWAS970377_Hcysteine-rich with EGF-like domain protein 1 measurement QTL GWAS970377 (human)3e-11cysteine-rich with EGF-like domain protein 1 measurement395150549515055Human
406970206GWAS619182_Hfibrinogen measurement QTL GWAS619182 (human)2e-08fibrinogen measurementblood fibrinogen level (CMO:0000209)395019589501959Human


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
1148 2265 2581 2036 4864 1467 1908 419 1298 259 2143 5746 5505 26 3701 617 1547 1392 166 1

Sequence


Ensembl Acc Id: ENST00000287585   ⟹   ENSP00000287585
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl39,498,361 - 9,553,822 (-)Ensembl
Ensembl Acc Id: ENST00000495730
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl39,550,612 - 9,552,307 (-)Ensembl
Ensembl Acc Id: ENST00000498277
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl39,552,572 - 9,553,795 (-)Ensembl
RefSeq Acc Id: NM_198560   ⟹   NP_940962
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3839,498,361 - 9,553,822 (-)NCBI
GRCh3739,540,045 - 9,595,486 (-)RGD
Build 3639,515,045 - 9,570,486 (-)NCBI Archive
Celera39,474,743 - 9,530,187 (-)RGD
HuRef39,476,796 - 9,532,110 (-)ENTREZGENE
CHM1_139,490,268 - 9,545,714 (-)NCBI
T2T-CHM13v2.039,490,279 - 9,545,747 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017006360   ⟹   XP_016861849
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3839,549,858 - 9,552,847 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054346461   ⟹   XP_054202436
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.039,541,604 - 9,544,772 (-)NCBI
Protein Sequences
Protein RefSeqs NP_940962 (Get FASTA)   NCBI Sequence Viewer  
  XP_016861849 (Get FASTA)   NCBI Sequence Viewer  
  XP_054202436 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAP37013 (Get FASTA)   NCBI Sequence Viewer  
  EAW63964 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000287585
  ENSP00000287585.6
GenBank Protein Q7Z7J7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_940962   ⟸   NM_198560
- UniProtKB: A6NH76 (UniProtKB/Swiss-Prot),   Q29RV7 (UniProtKB/Swiss-Prot),   Q7Z7J7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016861849   ⟸   XM_017006360
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSP00000287585   ⟸   ENST00000287585
RefSeq Acc Id: XP_054202436   ⟸   XM_054346461
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7Z7J7-F1-model_v2 AlphaFold Q7Z7J7 1-247 view protein structure

Promoters
RGD ID:6863458
Promoter ID:EPDNEW_H4894
Type:initiation region
Name:LHFPL4_1
Description:lipoma HMGIC fusion partner-like 4
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
GRCh3839,553,812 - 9,553,872EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:29568 AgrOrtholog
COSMIC LHFPL4 COSMIC
Ensembl Genes ENSG00000156959 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000287585 ENTREZGENE
  ENST00000287585.8 UniProtKB/Swiss-Prot
GTEx ENSG00000156959 GTEx
HGNC ID HGNC:29568 ENTREZGENE
Human Proteome Map LHFPL4 Human Proteome Map
InterPro LHFPL UniProtKB/Swiss-Prot
KEGG Report hsa:375323 UniProtKB/Swiss-Prot
NCBI Gene 375323 ENTREZGENE
OMIM 610240 OMIM
PANTHER LHFPL TETRASPAN SUBFAMILY MEMBER 4 PROTEIN UniProtKB/Swiss-Prot
  PTHR12489 UniProtKB/Swiss-Prot
Pfam L_HMGIC_fpl UniProtKB/Swiss-Prot
PharmGKB PA166351940 PharmGKB
UniProt A6NH76 ENTREZGENE
  LHPL4_HUMAN UniProtKB/Swiss-Prot
  Q29RV7 ENTREZGENE
  Q7Z7J7 ENTREZGENE
UniProt Secondary A6NH76 UniProtKB/Swiss-Prot
  Q29RV7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-06-27 LHFPL4  LHFPL tetraspan subfamily member 4    lipoma HMGIC fusion partner-like 4  Symbol and/or name change 5135510 APPROVED