SCYL3 (SCY1 like pseudokinase 3) - Rat Genome Database

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Gene: SCYL3 (SCY1 like pseudokinase 3) Homo sapiens
Analyze
Symbol: SCYL3
Name: SCY1 like pseudokinase 3
RGD ID: 1603625
HGNC Page HGNC:19285
Description: Predicted to enable ATP binding activity; identical protein binding activity; and protein kinase activity. Predicted to act upstream of or within inflammatory response; neuron differentiation; and protein localization. Located in several cellular components, including Golgi apparatus; endoplasmic reticulum; and lamellipodium.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: ezrin-binding partner PACE-1 (PACE-1); ezrin-binding protein PACE-1; PACE-1; PACE1; protein-associating with the carboxyl-terminal domain of ezrin; RP1-97P20.2; SCY1-like 3; SCY1-like protein 3; SCY1-like, kinase-like 3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381169,849,631 - 169,894,268 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1169,849,631 - 169,894,267 (-)EnsemblGRCh38hg38GRCh38
GRCh371169,818,772 - 169,863,037 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361168,088,854 - 168,129,661 (-)NCBINCBI36Build 36hg18NCBI36
Celera1142,931,586 - 142,972,865 (-)NCBICelera
Cytogenetic Map1q24.2NCBI
HuRef1141,044,727 - 141,085,609 (-)NCBIHuRef
CHM1_11171,244,369 - 171,285,280 (-)NCBICHM1_1
T2T-CHM13v2.01169,205,381 - 169,249,993 (-)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

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:11076863   PMID:12477932   PMID:12651155   PMID:15003124   PMID:15489334   PMID:15489336   PMID:16344560   PMID:16381901   PMID:16710414   PMID:18029348   PMID:19064610   PMID:20379614  
PMID:21188226   PMID:21653829   PMID:25416956   PMID:26638075   PMID:26673895   PMID:27880917   PMID:28514442   PMID:29509190   PMID:29568061   PMID:30021884   PMID:30639242   PMID:31056421  
PMID:31515488   PMID:31732153   PMID:32296183   PMID:32707033   PMID:33961781   PMID:34079125   PMID:34369648   PMID:34432599   PMID:34597346   PMID:35271311   PMID:35337019   PMID:35384245  
PMID:35844135   PMID:37232246  


Genomics

Comparative Map Data
SCYL3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381169,849,631 - 169,894,268 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1169,849,631 - 169,894,267 (-)EnsemblGRCh38hg38GRCh38
GRCh371169,818,772 - 169,863,037 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361168,088,854 - 168,129,661 (-)NCBINCBI36Build 36hg18NCBI36
Celera1142,931,586 - 142,972,865 (-)NCBICelera
Cytogenetic Map1q24.2NCBI
HuRef1141,044,727 - 141,085,609 (-)NCBIHuRef
CHM1_11171,244,369 - 171,285,280 (-)NCBICHM1_1
T2T-CHM13v2.01169,205,381 - 169,249,993 (-)NCBIT2T-CHM13v2.0
Scyl3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391163,756,669 - 163,782,695 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1163,756,669 - 163,782,695 (+)EnsemblGRCm39 Ensembl
GRCm381163,929,100 - 163,955,126 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1163,929,100 - 163,955,126 (+)EnsemblGRCm38mm10GRCm38
MGSCv371165,860,195 - 165,885,257 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361165,766,739 - 165,791,801 (+)NCBIMGSCv36mm8
Celera1166,370,534 - 166,395,607 (+)NCBICelera
Cytogenetic Map1H2.1- H2.2NCBI
cM Map171.23NCBI
Scyl3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81378,811,595 - 78,836,202 (+)NCBIGRCr8
mRatBN7.21376,278,428 - 76,303,038 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1376,278,428 - 76,301,716 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1378,896,495 - 78,919,783 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01380,200,830 - 80,224,120 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01377,455,414 - 77,478,704 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01382,230,938 - 82,255,640 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1382,231,030 - 82,254,318 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01387,103,921 - 87,128,610 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41379,687,546 - 79,710,834 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11379,704,000 - 79,724,634 (+)NCBI
Celera1376,012,137 - 76,035,426 (+)NCBICelera
Cytogenetic Map13q23NCBI
Scyl3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554627,448,893 - 7,476,840 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554627,443,841 - 7,477,596 (+)NCBIChiLan1.0ChiLan1.0
SCYL3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2179,855,292 - 79,912,359 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1179,541,059 - 79,584,939 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01145,299,266 - 145,383,511 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11149,056,553 - 149,100,201 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1149,057,194 - 149,095,445 (-)Ensemblpanpan1.1panPan2
SCYL3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1728,751,604 - 28,796,042 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl728,751,707 - 28,795,756 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha728,283,039 - 28,327,661 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0728,553,281 - 28,597,911 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl728,553,472 - 28,597,906 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1728,401,988 - 28,446,611 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0728,437,213 - 28,481,830 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0728,673,927 - 28,718,589 (+)NCBIUU_Cfam_GSD_1.0
Scyl3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934498,949,491 - 98,982,060 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648116,800,286 - 16,828,194 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648116,796,044 - 16,828,809 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCYL3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl481,134,352 - 81,175,536 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1481,134,035 - 81,175,537 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2488,760,885 - 88,802,370 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCYL3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12559,157,208 - 59,215,074 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2559,156,992 - 59,198,614 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605560,812,493 - 60,873,673 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scyl3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248267,749,332 - 7,779,145 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248267,748,995 - 7,783,157 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SCYL3
29 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 copy number gain See cases [RCV000051856] Chr1:164922655..180061589 [GRCh38]
Chr1:164891892..180030724 [GRCh37]
Chr1:163158516..178297347 [NCBI36]
Chr1:1q23.3-25.2		 pathogenic
GRCh38/hg38 1q24.2-25.1(chr1:168314822-175299299)x1 copy number loss See cases [RCV000053918] Chr1:168314822..175299299 [GRCh38]
Chr1:168284060..175268435 [GRCh37]
Chr1:166550684..173535058 [NCBI36]
Chr1:1q24.2-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1 copy number loss See cases [RCV000053914] Chr1:161740907..173965154 [GRCh38]
Chr1:161710697..173934292 [GRCh37]
Chr1:159977321..172200915 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q23.3-24.3(chr1:164036599-171252077)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053916]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053916]|See cases [RCV000053916] Chr1:164036599..171252077 [GRCh38]
Chr1:164005836..171221216 [GRCh37]
Chr1:162272460..169487840 [NCBI36]
Chr1:1q23.3-24.3		 pathogenic
GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1 copy number loss See cases [RCV000053917] Chr1:166762832..175327423 [GRCh38]
Chr1:166732069..175296559 [GRCh37]
Chr1:164998693..173563182 [NCBI36]
Chr1:1q24.1-25.1		 pathogenic
NM_020423.6(SCYL3):c.660C>T (p.Thr220=) single nucleotide variant Malignant melanoma [RCV000059987] Chr1:169869005 [GRCh38]
Chr1:169838146 [GRCh37]
Chr1:168104770 [NCBI36]
Chr1:1q24.2		 not provided
GRCh38/hg38 1q24.2-25.2(chr1:169218236-178075834)x1 copy number loss See cases [RCV000137128] Chr1:169218236..178075834 [GRCh38]
Chr1:169187474..178044969 [GRCh37]
Chr1:167454098..176311592 [NCBI36]
Chr1:1q24.2-25.2		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1 copy number loss See cases [RCV000143292] Chr1:163382523..175877022 [GRCh38]
Chr1:163352313..175846158 [GRCh37]
Chr1:161618937..174112781 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1q24.2-25.3(chr1:169423492-180367623) copy number gain not provided [RCV000767621] Chr1:169423492..180367623 [GRCh37]
Chr1:1q24.2-25.3		 pathogenic
GRCh37/hg19 1q23.2-25.1(chr1:160369890-175796325) copy number loss not provided [RCV000767779] Chr1:160369890..175796325 [GRCh37]
Chr1:1q23.2-25.1		 pathogenic
GRCh37/hg19 1q23.3-25.3(chr1:161676893-184071723)x1 copy number loss See cases [RCV000447098] Chr1:161676893..184071723 [GRCh37]
Chr1:1q23.3-25.3		 pathogenic
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 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 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 1q23.2-25.2(chr1:159815642-177026983)x1 copy number loss not provided [RCV000736717] Chr1:159815642..177026983 [GRCh37]
Chr1:1q23.2-25.2		 pathogenic
Single allele deletion 1q24q25 microdeletion syndrome [RCV000754969] Chr1:169095250..175778910 [GRCh37]
Chr1:1q24.2-25.1		 pathogenic
NM_001320047.2(FIRRM):c.2342A>C (p.Glu781Ala) single nucleotide variant not provided [RCV000883591] Chr1:169851914 [GRCh38]
Chr1:169821055 [GRCh37]
Chr1:1q24.2		 benign
GRCh37/hg19 1q24.2-25.1(chr1:167430471-174635618)x1 copy number loss not provided [RCV001005149] Chr1:167430471..174635618 [GRCh37]
Chr1:1q24.2-25.1		 pathogenic
NM_020423.7(SCYL3):c.622C>G (p.Gln208Glu) single nucleotide variant Inborn genetic diseases [RCV003290348] Chr1:169870258 [GRCh38]
Chr1:169839399 [GRCh37]
Chr1:1q24.2		 uncertain significance
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
GRCh37/hg19 1q23.3-24.3(chr1:162330810-171532331) copy number loss not specified [RCV002053680] Chr1:162330810..171532331 [GRCh37]
Chr1:1q23.3-24.3		 pathogenic
GRCh37/hg19 1q24.2-24.3(chr1:167391422-171843613) copy number loss not specified [RCV002053691] Chr1:167391422..171843613 [GRCh37]
Chr1:1q24.2-24.3		 pathogenic
NC_000001.10:g.(?_169660781)_(170521603_?)del deletion not provided [RCV001972554] Chr1:169660781..170521603 [GRCh37]
Chr1:1q24.2		 pathogenic
NM_020423.7(SCYL3):c.520A>T (p.Met174Leu) single nucleotide variant Inborn genetic diseases [RCV002749288] Chr1:169873698 [GRCh38]
Chr1:169842839 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1670A>C (p.Glu557Ala) single nucleotide variant Inborn genetic diseases [RCV002879598] Chr1:169854607 [GRCh38]
Chr1:169823748 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1313-836G>C single nucleotide variant Inborn genetic diseases [RCV002997860] Chr1:169855800 [GRCh38]
Chr1:169824941 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.704C>T (p.Ala235Val) single nucleotide variant Inborn genetic diseases [RCV002732025] Chr1:169868961 [GRCh38]
Chr1:169838102 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1726G>T (p.Asp576Tyr) single nucleotide variant Inborn genetic diseases [RCV002762778] Chr1:169854551 [GRCh38]
Chr1:169823692 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1313-894G>A single nucleotide variant Inborn genetic diseases [RCV002737696] Chr1:169855858 [GRCh38]
Chr1:169824999 [GRCh37]
Chr1:1q24.2		 likely benign
NM_020423.7(SCYL3):c.1313-919T>G single nucleotide variant Inborn genetic diseases [RCV002757611] Chr1:169855883 [GRCh38]
Chr1:169825024 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1807G>A (p.Glu603Lys) single nucleotide variant Inborn genetic diseases [RCV002704508] Chr1:169854470 [GRCh38]
Chr1:169823611 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1782G>C (p.Lys594Asn) single nucleotide variant Inborn genetic diseases [RCV002784961] Chr1:169854495 [GRCh38]
Chr1:169823636 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1576A>G (p.Thr526Ala) single nucleotide variant Inborn genetic diseases [RCV002984325] Chr1:169854701 [GRCh38]
Chr1:169823842 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.24A>C (p.Leu8Phe) single nucleotide variant Inborn genetic diseases [RCV002892331] Chr1:169888817 [GRCh38]
Chr1:169857958 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1984T>C (p.Phe662Leu) single nucleotide variant Inborn genetic diseases [RCV002803648] Chr1:169854293 [GRCh38]
Chr1:169823434 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1711C>T (p.Leu571Phe) single nucleotide variant Inborn genetic diseases [RCV002742803] Chr1:169854566 [GRCh38]
Chr1:169823707 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1918G>A (p.Glu640Lys) single nucleotide variant Inborn genetic diseases [RCV002874614] Chr1:169854359 [GRCh38]
Chr1:169823500 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.200G>A (p.Arg67Lys) single nucleotide variant Inborn genetic diseases [RCV002832330] Chr1:169878785 [GRCh38]
Chr1:169847926 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.76G>A (p.Val26Ile) single nucleotide variant Inborn genetic diseases [RCV002940948] Chr1:169888765 [GRCh38]
Chr1:169857906 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1313-939A>T single nucleotide variant Inborn genetic diseases [RCV003185771] Chr1:169855903 [GRCh38]
Chr1:169825044 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1587C>G (p.Asn529Lys) single nucleotide variant Inborn genetic diseases [RCV003214857] Chr1:169854690 [GRCh38]
Chr1:169823831 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.526C>T (p.Pro176Ser) single nucleotide variant Inborn genetic diseases [RCV003185432] Chr1:169870354 [GRCh38]
Chr1:169839495 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.1313-984T>C single nucleotide variant Inborn genetic diseases [RCV003378094] Chr1:169855948 [GRCh38]
Chr1:169825089 [GRCh37]
Chr1:1q24.2		 uncertain significance
GRCh37/hg19 1q23.3-25.1(chr1:164571371-175708060)x1 copy number loss not provided [RCV003483966] Chr1:164571371..175708060 [GRCh37]
Chr1:1q23.3-25.1		 pathogenic
GRCh37/hg19 1q24.2-31.1(chr1:167994071-187711459)x1 copy number loss not specified [RCV003987250] Chr1:167994071..187711459 [GRCh37]
Chr1:1q24.2-31.1		 pathogenic
NM_020423.7(SCYL3):c.456C>A (p.Ala152=) single nucleotide variant not provided [RCV003409238] Chr1:169875987 [GRCh38]
Chr1:169845128 [GRCh37]
Chr1:1q24.2		 likely benign
NM_020423.7(SCYL3):c.965A>T (p.Gln322Leu) single nucleotide variant Inborn genetic diseases [RCV002831466] Chr1:169862788 [GRCh38]
Chr1:169831929 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_020423.7(SCYL3):c.157G>A (p.Ala53Thr) single nucleotide variant Inborn genetic diseases [RCV003371116] Chr1:169888684 [GRCh38]
Chr1:169857825 [GRCh37]
Chr1:1q24.2		 uncertain significance
NM_001320047.2(FIRRM):c.2249G>A (p.Gly750Glu) single nucleotide variant not provided [RCV003409236] Chr1:169851821 [GRCh38]
Chr1:169820962 [GRCh37]
Chr1:1q24.2		 likely benign
NM_020423.7(SCYL3):c.1047T>C (p.His349=) single nucleotide variant not provided [RCV003409237] Chr1:169862706 [GRCh38]
Chr1:169831847 [GRCh37]
Chr1:1q24.2		 likely benign
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR149hsa-miR-149-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248

Predicted Target Of
Summary Value
Count of predictions:2245
Count of miRNA genes:886
Interacting mature miRNAs:1012
Transcripts:ENST00000367770, ENST00000367771, ENST00000367772, ENST00000423670, ENST00000470238
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.

Markers in Region
SHGC-75868  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371169,827,771 - 169,827,928UniSTSGRCh37
Build 361168,094,395 - 168,094,552RGDNCBI36
Celera1142,937,555 - 142,937,712RGD
Cytogenetic Map1q24.2UniSTS
HuRef1141,050,285 - 141,050,442UniSTS
GeneMap99-GB4 RH Map1611.78UniSTS
RH103578  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371169,822,926 - 169,823,101UniSTSGRCh37
Build 361168,089,550 - 168,089,725RGDNCBI36
Celera1142,932,708 - 142,932,883RGD
Cytogenetic Map1q24.2UniSTS
HuRef1141,045,438 - 141,045,613UniSTS
GeneMap99-GB4 RH Map1612.71UniSTS
SHGC-106696  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371169,839,166 - 169,839,443UniSTSGRCh37
Build 361168,105,790 - 168,106,067RGDNCBI36
Celera1142,948,951 - 142,949,228RGD
Cytogenetic Map1q24.2UniSTS
HuRef1141,061,671 - 141,061,948UniSTS
SHGC-75871  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371169,822,074 - 169,822,179UniSTSGRCh37
Build 361168,088,698 - 168,088,803RGDNCBI36
Celera1142,931,856 - 142,931,961RGD
Cytogenetic Map1q24.2UniSTS
HuRef1141,044,586 - 141,044,691UniSTS
GeneMap99-GB4 RH Map1618.37UniSTS
GeneMap99-GB4 RH Map1612.71UniSTS
Whitehead-RH Map1761.1UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 70 12 207 36 406 29 309 26 131 42 239 254 10 9 230 3 1
Low 2369 2893 1518 588 1514 436 4048 2117 3560 376 1221 1359 165 1 1195 2558 3 1
Below cutoff 86 1 31 54 43 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_020423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_181093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006711465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011509801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011509802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011509803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017001865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024448565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047425909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054337797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001737335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001737336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA844031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF540957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK292507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK304481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL031297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL117233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY144493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC014662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX647352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA449356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB285397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT584301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000367770   ⟹   ENSP00000356744
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,853,074 - 169,888,888 (-)Ensembl
RefSeq Acc Id: ENST00000367771   ⟹   ENSP00000356745
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,849,631 - 169,893,896 (-)Ensembl
RefSeq Acc Id: ENST00000367772   ⟹   ENSP00000356746
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,853,074 - 169,893,959 (-)Ensembl
RefSeq Acc Id: ENST00000423670   ⟹   ENSP00000407993
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,854,511 - 169,894,267 (-)Ensembl
RefSeq Acc Id: ENST00000470238
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,859,119 - 169,893,952 (-)Ensembl
RefSeq Acc Id: NM_020423   ⟹   NP_065156
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,893,896 (-)NCBI
GRCh371169,822,215 - 169,863,100 (-)NCBI
Build 361168,088,854 - 168,129,661 (-)NCBI Archive
Celera1142,931,586 - 142,972,865 (-)RGD
HuRef1141,044,727 - 141,085,609 (-)NCBI
CHM1_11171,244,369 - 171,285,280 (-)NCBI
T2T-CHM13v2.01169,205,381 - 169,249,621 (-)NCBI
Sequence:
RefSeq Acc Id: NM_181093   ⟹   NP_851607
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,893,896 (-)NCBI
GRCh371169,822,215 - 169,863,100 (-)NCBI
Build 361168,088,965 - 168,124,657 (-)NCBI Archive
Celera1142,931,586 - 142,972,865 (-)RGD
HuRef1141,044,727 - 141,085,609 (-)NCBI
CHM1_11171,244,369 - 171,285,280 (-)NCBI
T2T-CHM13v2.01169,205,381 - 169,249,621 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006711465   ⟹   XP_006711528
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,893,896 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011509801   ⟹   XP_011508103
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,894,268 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011509802   ⟹   XP_011508104
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,888,728 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017001862   ⟹   XP_016857351
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,893,896 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017001863   ⟹   XP_016857352
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,849,631 - 169,894,268 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047425909   ⟹   XP_047281865
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,854,816 - 169,893,896 (-)NCBI
RefSeq Acc Id: XM_054337792   ⟹   XP_054193767
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01169,205,381 - 169,249,690 (-)NCBI
RefSeq Acc Id: XM_054337793   ⟹   XP_054193768
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01169,205,381 - 169,249,993 (-)NCBI
RefSeq Acc Id: XM_054337794   ⟹   XP_054193769
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01169,205,381 - 169,249,689 (-)NCBI
RefSeq Acc Id: XM_054337795   ⟹   XP_054193770
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01169,205,381 - 169,249,993 (-)NCBI
RefSeq Acc Id: XM_054337796   ⟹   XP_054193771
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01169,205,381 - 169,244,453 (-)NCBI
RefSeq Acc Id: XM_054337797   ⟹   XP_054193772
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01169,210,550 - 169,249,621 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_065156   ⟸   NM_020423
- Peptide Label: isoform 1
- UniProtKB: X6RHX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_851607   ⟸   NM_181093
- Peptide Label: isoform 2
- UniProtKB: Q96C56 (UniProtKB/Swiss-Prot),   Q8IZN9 (UniProtKB/Swiss-Prot),   Q5THA8 (UniProtKB/Swiss-Prot),   Q5THA6 (UniProtKB/Swiss-Prot),   A8K8Z2 (UniProtKB/Swiss-Prot),   Q9UBK6 (UniProtKB/Swiss-Prot),   Q8IZE3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006711528   ⟸   XM_006711465
- Peptide Label: isoform X1
- UniProtKB: Q96C56 (UniProtKB/Swiss-Prot),   Q8IZN9 (UniProtKB/Swiss-Prot),   Q5THA8 (UniProtKB/Swiss-Prot),   Q5THA6 (UniProtKB/Swiss-Prot),   A8K8Z2 (UniProtKB/Swiss-Prot),   Q9UBK6 (UniProtKB/Swiss-Prot),   Q8IZE3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011508103   ⟸   XM_011509801
- Peptide Label: isoform X1
- UniProtKB: Q96C56 (UniProtKB/Swiss-Prot),   Q8IZN9 (UniProtKB/Swiss-Prot),   Q5THA8 (UniProtKB/Swiss-Prot),   Q5THA6 (UniProtKB/Swiss-Prot),   A8K8Z2 (UniProtKB/Swiss-Prot),   Q9UBK6 (UniProtKB/Swiss-Prot),   Q8IZE3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011508104   ⟸   XM_011509802
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_016857352   ⟸   XM_017001863
- Peptide Label: isoform X2
- UniProtKB: X6RHX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016857351   ⟸   XM_017001862
- Peptide Label: isoform X2
- UniProtKB: X6RHX1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000407993   ⟸   ENST00000423670
RefSeq Acc Id: ENSP00000356746   ⟸   ENST00000367772
RefSeq Acc Id: ENSP00000356745   ⟸   ENST00000367771
RefSeq Acc Id: ENSP00000356744   ⟸   ENST00000367770
RefSeq Acc Id: XP_047281865   ⟸   XM_047425909
- Peptide Label: isoform X4
RefSeq Acc Id: XP_054193770   ⟸   XM_054337795
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054193768   ⟸   XM_054337793
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054193767   ⟸   XM_054337792
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054193769   ⟸   XM_054337794
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054193771   ⟸   XM_054337796
- Peptide Label: isoform X3
RefSeq Acc Id: XP_054193772   ⟸   XM_054337797
- Peptide Label: isoform X4
Protein Domains
Protein kinase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8IZE3-F1-model_v2 AlphaFold Q8IZE3 1-742 view protein structure

Promoters
RGD ID:6786804
Promoter ID:HG_KWN:6126
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_181093,   OTTHUMT00000087548,   OTTHUMT00000087549,   OTTHUMT00000087552,   UC001GGU.2
Position:
Human AssemblyChrPosition (strand)Source
Build 361168,129,546 - 168,130,197 (-)MPROMDB
RGD ID:6858082
Promoter ID:EPDNEW_H2206
Type:initiation region
Name:SCYL3_1
Description:SCY1 like pseudokinase 3
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
GRCh381169,893,896 - 169,893,956EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:19285 AgrOrtholog
COSMIC SCYL3 COSMIC
Ensembl Genes ENSG00000000457 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000367770.5 UniProtKB/Swiss-Prot
  ENST00000367771 ENTREZGENE
  ENST00000367771.11 UniProtKB/Swiss-Prot
  ENST00000367772 ENTREZGENE
  ENST00000367772.8 UniProtKB/Swiss-Prot
  ENST00000423670 ENTREZGENE
  ENST00000423670.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transferase(Phosphotransferase) domain 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000000457 GTEx
HGNC ID HGNC:19285 ENTREZGENE
Human Proteome Map SCYL3 Human Proteome Map
InterPro ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HEAT_type_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:57147 UniProtKB/Swiss-Prot
NCBI Gene 57147 ENTREZGENE
OMIM 608192 OMIM
PANTHER PROTEIN-ASSOCIATING WITH THE CARBOXYL-TERMINAL DOMAIN OF EZRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SCY1-RELATED S/T PROTEIN KINASE-LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PK_Tyr_Ser-Thr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142670945 PharmGKB
PROSITE HEAT_REPEAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A8K8Z2 ENTREZGENE
  PACE1_HUMAN UniProtKB/Swiss-Prot
  Q5THA6 ENTREZGENE
  Q5THA8 ENTREZGENE
  Q8IZE3 ENTREZGENE
  Q8IZN9 ENTREZGENE
  Q96C56 ENTREZGENE
  Q9UBK6 ENTREZGENE
  X6RHX1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A8K8Z2 UniProtKB/Swiss-Prot
  Q5THA6 UniProtKB/Swiss-Prot
  Q5THA8 UniProtKB/Swiss-Prot
  Q8IZN9 UniProtKB/Swiss-Prot
  Q96C56 UniProtKB/Swiss-Prot
  Q9UBK6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-29 SCYL3  SCY1 like pseudokinase 3    SCY1-like, kinase-like 3  Symbol and/or name change 5135510 APPROVED
2015-07-28 SCYL3  SCY1-like, kinase-like 3    SCY1-like 3 (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED
2012-07-05 SCYL3  SCY1-like 3 (S. cerevisiae)  SCYL3  SCY1-like 3 (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED